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Scientific Method for the Non-Scientist? Yes, please! (from Kausik Datta's blog)

Fri, 07/13/2012 - 10:09pm

NextGen Voices is a feature of the premier science magazine, Science. It is designed as a series of surveys targeted towards young scientists, asking them questions on different aspects of life as a scientist that matters to them.(For some reason, it is not very well publicized, which is a pity – because I do think that NextGen Voices is offering young scientists an important platform to voice their opinions. I got to know about it only because my colleague in the lab, a subscriber to Science, showed it to me. This is partly the reason why I wanted to blog on this today – to raise awareness).

In 250 words or less, NextGen Voices asks young scientists:
What one big idea in your field do you wish that every non-scientist understood? Why?

I had a little time in between incubations sigh!, and decided to quickly jot down a response. I am sure there would be many other worthy folks who would write awesome essays on what matters to them. I can’t compete with them. But this survey question immediately lit up a corner of my mind like the tree at the Rockefeller Center around Christmas time (see Postscript); that is to say, this topic – which is associated with communication and perception of science – is very dear to me. The following is what I wrote:

A scientific idea that I wish every non-scientist understood? Easy: “Scientific Method”, the foundation for rational, empirical, evidence-based understanding of the natural world; the central idea elegantly guiding how science works to advance knowledge.

To an enquiring mind, systematic observations of natural phenomena raise questions about their characteristics, antecedents and effects. To seek answers, the Method requires formulation of one or several ‘hypotheses’ – each a speculation about a phenomenon’s properties – including a ‘null hypothesis’, the idea that an observed phenomenon is merely a coincidental product of pure chance. Validity of each hypothesis is tested empirically by designing and conducting experiments with rigorous scientific controls, and analyzing generated data objectively to gather evidence.

A hypothesis unsupportable by evidence is modified (and retested), or discarded altogether, making way for alternative hypotheses. If supported by evidence, the hypothesis is accepted and forms the basis for asking new questions. Either way, this process continues recursively until there is a measure of confidence in the observations. Thus is born a ‘scientific theory’, a punctiliously arrived-at, confirmed and reliable explanation for natural phenomena.

Unfortunately, several key terms, ‘theory’ among them, have entered common parlance in a way that allows only their narrow, most restrictive definitions; for instance, ‘theory’ conjures up, to the lay mind, an image of unproven assertions. This severely hampers public perception of science’s accomplishments, leading to challenges to the credibility of scientific conclusions – as seen, for example, in the antagonism towards evolution, vaccines and global warming. This is eventually detrimental to the society.

For want of space (brevity ain’t my strong suite!), I couldn’t talk about another central idea, falsifiability or refutability. A hypothesis, in order to be valid, must be falsifiable, which means that whatever the hypothesis, it must be possible, at least in principle, to design an experiment whose outcome would completely contradict or refute the assertion made in it. For example, ‘All dogs are friendly’ is a testable, falsifiable hypothesis because it is logically possible that some dogs may not be friendly, and the actual finding of even one such canine would refute the hypothesis.

Why is this important? As human beings, even scientists may suffer from certain cognitive biases, including confirmation bias – a situation in which a preexisting belief in a given hypothesis pushes one to subconsciously filter observations in order to retain only those that are supportive of the hypothesis, even if the empirical reality demonstrates otherwise. An appropriate example of confirmation bias is an enduring belief in scientifically implausible propositions, such as homeopathy, in face of all evidence pointing otherwise.

By adhering to the principle of falsifiability, a scientist is obliged to strive to disprove a hypothesis, rather than prove it. This, along with an emphasis on reproducibility of results and the maintenance of strict controls during experiments, can adequately alleviate such cognitive biases, making the scientific conclusions that much stronger.


P.S. A glimpse of the 2004 Christmas Tree at the Rockefeller Center, New York City (click on the photo to embiggen).

P.P.S. Do add your voice by clicking on the NextGen Voices link at the beginning of this post.

Curvature of the Earth (cartoon) (from Viktor Poor's blog)

Wed, 07/11/2012 - 7:35am

Todays cartoon inspired by the phenomenon that due to the curvature of the globe, distant objects are hidden in the ocean. This picture explains it:HorizonDistance.pngImage source: Wikipedia course, there is a twist in the story:curve of the glbe.pngThe other source of inspiration is the relative size of swimming pools. About a year I started to swim regularly. At the first times even one lap seemed utterly long, I was out of breath. Now, I can swim about 4 kilometers without any problem.Good news! I finally started the official Facebook page of Stripped Science at facebook.com/strippedscience

"This is not what we expected" said Julie Brigham-Grette in video describing work at Lake El'gygytgyn. (from Liz O'Connell's blog)

Tue, 07/10/2012 - 3:26pm

LakeE_meteorite.jpgFairbanks, Alaska, July 10, 2012—- “To this point no one has much of any terrestrial record anywhere in the Arctic older than 125,000 years ago,” said Julie Brigham-Grette, University of Massachusetts Amherst as she describes findings from the Lake El’gygytgyn (or Lake E) project to Office of Polar Programs Board Meeting at the National Science Foundation.LakeE_pipes.jpgBrigham-Grette along with Martin Melles, University of Cologne Germany and Pavel Minyuk, North-East Interdisciplinary Scientific Research Institute in Magadan, Russia, undertook the core drilling of Lake E, a lake that sits today inside a basin formed by a meteorite that struck the earth 3.6 million years ago. From their findings so far Brigham-Grette confidently said, “This is not a back water lake in the middle of nowhere—it’s actually a lake that is recording a global signal.”LakeE_trio.jpgScience magazine published 2.8 Million Years of Arctic Climate Change from Lake El’gygytgyn, NE Russia (Science online 21 June 2012, in print July 13) describing some of the team’s findings. But watch the video JBG Describes Research at Lake E to see and hear the enthusiasm and details as Brigham-Grette describes the findings of this remarkable discovery.LakeE_group.jpg Frontier Scientists shares first person accounts and real time insights from leading archaeologists, grizzly bear biologists, volcano researchers, climate change specialists and other scientists.The research covers many categories:Arctic Archaeologythe Arctic’s Amazing BirdsClimate Change WatchComputational ScienceCook Inlet VolcanoesGrizzliesPaleo-Eskimo HistoryPermafrostPetroglyphsAlaska’s Unmanned Aircraft ResearchAlutiiq WeaversWhere Is Lake El’Gygytgyn?*Arctic Winter Cruise“We want to let travelers, teachers, students, aspiring scientists, and anyone else interested in science feel as if they are with scientists as they track grizzlies or take the temperature of permafrost in a borehole,” explained Liz O’Connell, video director for Frontier Scientists.Visitors to Frontier Scientists can ask questions direct to our featured scientist. Fascinating video of current scientific discoveries in some of the Arctic’s most remote and dramatic landscapes are chronicled in short videos, Twitter feeds, blogs and web reports. Discover Arctic science at www.FrontierScientists.com.

Sticking together--Epidermal Lipids and Research Collaborations (from Lowell Goldsmith's blog)

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

5856660723_ef2b89a8e6_m--by--Images_of_Money-on-Flickr.jpgWhile a resident at Harvard (Massachusetts General Hospital) in Howard Baden’s lab I was assigned a research project studying human epidermal lipids using X-ray diffraction techniques. Pounds of scale that Howard Baden and Irwin Freedberg had collected from patients with erythroderma were extracted with chloroform and methanol over steam baths, and analyzed for lipids by various techniques. These studies culminated in a presentation to the Society for Investigative Dermatology in Atlantic City and publication in Nature; and the idea that a lifetime in the dermatological sciences would be so much fun was instilled.I have retained a special interest in epidermal lipids. Recently, Iwai et al published a detailed study in JID using various physical, spectrographic, and imaging techniques to study lipids associated with the barrier. They present a new model of how cholesterol and ceramide sphingoids are arranged in the barrier to support its various functions. I will leave the details of the scientific results to the aficionados and concentrate instead on the organization and internationalization of science exemplified by this project.The main players come from Northern Europe (Sweden, Norway, and the United Kingdom) and Japan, and there was close collaboration between researchers from Academia and Industry in a project that spanned a decade. Is a project of this long duration, involving individuals from multiple institutions and countries, the public (non-profit) sector and the for-profit sector the new norm? In the 75th Anniversary issue of JID, Bauer and Cohen and Parrish discuss increasing industrial and academic collaborations; these articles are required reading for those thinking about commercializing their scientific findings and collaborating with the for-profit sector. In the same issue, Uitto and Rodeck discuss the globalization of the research enterprise.All institutions must address for themselves the advantages, disadvantages, and barriers to various collaborations. The role of confidentiality, protection of graduate students, and the role of intellectual property must all be considered. In addition, is there a convergence of interests, with academic institutions concerned about commercialization, spinning off companies, and fostering biotech incubators? Is that the best model and direction for academic institutions? What are the best models: for the academic institution, for the investigator?Our scientific societies should encourage these discussions. Models should be explored, and the excellent – and disastrous — outcomes discussed. Yes, everyone likes to talk about successful collaborations, but failures require as much if not more consideration, even if the discussion is painful and difficult. Seeking profits and patents may complicate or even prevent frank discussions; is that the kind of environment that scientists in academia ultimately desire? These questions lack easy answers, but if they are never asked they will never be answered and the framework for best practices will not be established. Parrish’s article concludes with an important checklist of the institutional, personnel, and leadership issues to consider when beginning new collaborative endeavors. It deserves attention. We encourage readers to comment on their experiences in this important interface between the for-profit and not-for-profit worlds.TO COMMENT:

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Image used under the Creative Commons License; the original can be found at Images_of_Money on Flickr.com

A Trip Into the Swamps (from Paige Brown's blog)

Mon, 07/09/2012 - 1:39pm

20120701-IMG_9436_NG.jpg Cypress Trees and knees at dusk in the Atchafalaya Basin, Louisiana.A trip into Atchafalaya Basin in Bayou Sorrel, Louisiana is a surreal experience. Between the softly dressed cypress trees covered in Spanish moss, the calm green waters, and the unique species of birds perched atop majestic water-dwelling trees, you feel that you’ve just stepped into an enchanted forest. I traveled with my boyfriend’s family into these swamps in a 6-seater boat, guided by a Basinkeeper who knows well the value of this region to local wildlife and human populations both.The Atchafalaya Basin is the largest swamp in the United States. A combination of wetlands and river delta area where the Atchafalaya River and the Gulf of Mexico converge, this swamp naturally protects Louisiana’s coast from the hurricanes that are notorious here. Every 2.7 miles of wetlands may absorb an average of one foot of storm surge (USACE, 1963). But these beautiful swamps deserve a look beneath the surface. Beyond their beauty, the Louisiana wetlands play important roles in ecosystem services and protection of the state’s coastline08functions.htm. These wetlands and the cypress trees that populate them, as shown here, act to naturally protect the coastline from erosion and hurricane damage, to store and convey floodwaters, and to absorb sediments and contaminants. Swamps and wetlands are some of the largest natural carbon sinks in the world, sequestering excess carbon dioxide that would otherwise drive further climatic warming.But the swamps and wetlands of south Louisiana are in peril. Between oil pumping, agricultural pressures, human transportation, and illegal cypress tree logging, the rate of wetland loss here exceeds the equivalent of a football field every hour. 80% of U.S. coastal land loss is occurring right here in Louisiana, largely due to human disturbance to these wetlands.Levees along the Mississippi river have for decades now starved the Louisiana wetlands of the natural sediments that used to flow into them. Starving wetlands are sinking in a phenomenon known as natural land subsidence, while pumping the ground underneath for oil is only aggravating the problem. Illegal logging and death of the cypress trees in these swamps reduces the buffering capacity of the Basin against hurricane and storm surge damages to urban areas. Learn more about what is causing the land loss crisis here.Global warming is aggravating the loss of wetlands, while dying wetlands release even more carbon dioxide, a greenhouse gas, into the atmosphere in a vicious cycle of climatic forcing. Global warming increases the likelihood of highly-damaging hurricanes that flood and damage these wetlands, while rising sea levels due to glacial melting and ocean warming pose further threats to the swamps.Criss-crossing canals cut into the swamps create ‘spoil banks’ that destroy the natural hydrology of the region, preventing natural movement of water through the Basin. Invasive plant and animal species have also taken their toll on these delicate swamps.Destroying these wetlands in the name of industrial progress and oil resources has serious consequences for local ecosystems. Louisiana’s wetlands provide habitats for thousands of unique plant and animal species, many of which are now endangered. Louisiana black bears, bald eagles, brown pelicans, ibises with long down curved bills, great white egrets and blue herons wading with their slender legs through marshy waters in search of fish. Between food, fuel, pollution interception, coastal protection and flood control, the value of healthy Louisiana swamps and wetlands tops millions of dollars.Here, locals fish while telling tales of old days when these swamps were dark from thick canopies and the singing of birds was deafening. Today, the Basinkeeper who gave us this tour fights against illegal cypress tree logging and other wetland degradation forces.Please enjoy this gallery of pictures I took of the Atchafalaya Swamp! All pictures belong to Paige Brown, @FromTheLabBench. Please provide attribution. Follow @1restorethegulf and visit www.restorethegulf.com to sign a petition to help restore America’s Gulf. ___20120701-IMG_9344_NG.jpgA spontaneous fishing moment!_20120701-IMG_9381_NG.jpgMighty Cypress Tree.20120701-DSCN5920.jpgGreen Heron in the swamps.20120701-IMG_9359.jpgA flock of American white ibises above.20120701-IMG_9474.jpgAn abandoned oil field production facility in Atchafalaya Basin.__20120701-IMG_9407_NG.jpgCommon Salvinia, or Water Spangles, an invasive plant species in these swamps. Accidentally introduced to this region, this species forms a dense cover over the swamps and depletes dissolved oxygen in the waters, degrading habitats and causing fish kills.

Quality over quantity (from Peter Etchells' blog)

Mon, 07/09/2012 - 10:03am

Darwin’s theory of Natural Selection. Einstein’s theory of general relativity. Watson and Crick’s description of the DNA molecule. All of these, and many more, are easily classed as some of Science’s Greatest Discoveries. But with modern pressures to publish high-impact papers as often as possible, are the opportunities to find the next Great Scientific Discoveries being stifled?As I’ve mentioned before, last year one of the academic heavyweights of social psychology, Diederik Stapel, was found guilty of faking data in a lot of his research. Quite a lot of data, actually – over 30 scientific papers and numerous PhD theses. In the aftermath, a lot of difficult questions have been asked about how and why something like this could possibly happen. Some of the reasoning behind his actions comes from Stapel himself: “…I did not withstand the pressure to score, to publish, the pressure to get better in time. I wanted too much, too fast. In a system where there are few checks and balances, where people work alone, I took the wrong turn.” Stapel’s behaviour is quite clearly inexcusable, but the pressure to publish may feel familiar to many other researchers – perhaps, most acutely, by the one hundred academics who recently lost their jobs at the University of Sydney for not publishing frequently enough. In principle, the idea of publishing as much as possible doesn’t seem too bad – if you’re running lots of experiments and doing lots of work, it means that we might get to see those Great Scientific Discoveries quicker, right? But this sort of mentality can cause (and has already caused) a number of undesirable side effects. Perhaps the most well known is ‘publication bias’. This can manifest itself in different ways, but generally refers to the tendency for positive results (in other words, those in which a hypothesis is confirmed) to be much more likely to be published than negative, or inconclusive results. Put another way, if you run a perfectly good, well-designed experiment, but your analysis comes up with a null result, you’re much less likely to get it published, or even actually submit it for publication. This is bad, because it means that the total body of research that does get published on a particular topic might be completely unrepresentative of what’s actually going on. It can be a particular issue for medical science – say, for example, I run a trial for a new behavioural therapy that’s supposed to completely cure anxiety. My design is perfectly robust, but my results suggest that the therapy doesn’t work. That’s a bit boring, and I don’t think it will get published anywhere that’s considered prestigious, so I don’t bother writing it up; the results just get stashed away in my lab, and maybe I’ll come back to it in a few years. But what if labs in other institutions run the same experiment? They don’t know I’ve already done it, so they just carry on with it. Most of them find what I found, and again don’t bother to publish their results – it’s a waste of time. Except a couple of labs did find that the therapy works. They report their experiments, and now it looks like we have good evidence for a new and effective anxiety therapy, despite the large body of (unpublished) evidence to the contrary.This leads into all sorts of issues rooted in precisely how we statistically analyse our work, but there’s another, simpler problem that this phenomenon causes; it’s wasting a lot of time for a lot of people. There must be countless scientific studies out there that, whilst methodologically sound, simply just didn’t produce a result deemed interesting enough to publish. And because they weren’t published, we don’t have a measure of how many times they’ve inadvertently been replicated elsewhere. Compounding this problem is the idea that if, say, a particularly time-intensive experiment doesn’t work out, researchers might find themselves under pressure to quickly publish something else instead; something that might not be particularly interesting or useful, but is quick, easy, and likely to have a positive outcome. The end result is that we’re sacrificing scientific creativity and research diversity for safe options, science in small increments, and administrative box-ticking. In Psychology, projects like Psychfiledrawer are starting to address this issue, but more clearly needs to be done.We have to accept, and be comfortable with, the fact that theories and ideas need time to fully develop. As scientists, we to be okay with things when they don’t work out the way we thought they would. The world is a big, noisy, messy place, and not only is that absolutely fine, it’s also exciting. Darwin’s theories on evolution were almost 23 years in the making; would the modern-day pressure to publish have meant that On the Origin of the Species might have been confined to a dusty lab drawer, in favour of a quick and easy, but perhaps mediocre, paper?

Back into view IV (or: Continuing exercises in futility) (from Lee Turnpenny's blog)

Sat, 07/07/2012 - 1:11pm

In my Inbox this morning, a Jobsite Jobs-by-Email Alert for ‘Post Production Editor’. Money not great, but in (what I remember as) a nicer town than my current residence, so I clicked for details, wherein the Job Summary immediately informed that the recruiting organisation is God TV having filtered out most of the ‘lying-for-a-living’ crap that was finding its way through and taking up too much of my time sifting and deleting, it seems these things are not leakproof. Because, although the terms ‘advertising’/‘marketing’/‘PR’ do not figure in the summary, what they do require is:bq. ‘… a dynamic & creative person who can edit original material which has been shot by the in-house production department and convey it’s true potential through creative flair and expertise in order to produce stunning promos & interstitials.’ (My emphasis in bold.)In other words… advertising_. (Shouldn’t that be ‘interstices’ as the noun? Unless they’re flogging imperfect crystals.) Well, being unfamiliar and intrigued, I took myself to the "_God TV site":http://www.god.tv/, where you can read all about the mission, vision and beliefs espoused by God TV_’s Founders, the lovely Rory & Wendywendy (careful, Lee, you’re giving them publicity), who will be happy to accept your donations and partnership commitment levies on behalf of Angel Charities.The eleemosynary presentation and promotion of faith. None of which suckerdom interests me in the slightest. But I wonder whether the application process for jobs in this organisation requires some demonstration of endorsement of said mission, vision and beliefs. The job advert does not stipulate so – because, legally, it cannot. That would be discriminatory. I guess commencing the Job Summary with ‘God TV’ suffices as ‘The-ungodly-need-not-apply’ filter here.

Weathering the Storm Surge (from Paige Brown's blog)

Fri, 07/06/2012 - 12:34pm

Tropical cyclone-generated storm surges are among the most deadly and costly natural disasters to impact the United States. Storm surges occur as sea water is pushed up against a shoreline by hurricane winds, and are often the greatest threat to life and property from a hurricane.road_erosion.jpgBeachfront road and boardwalk damaged by Hurricane Jeanne (2004), posted by the National Hurricane Center. See a simulation of storm surge.Researchers at Louisiana State University in Baton Rouge, La, have created the first comprehensive database of storm surge information for small and large tropical cyclones alike to hit the Gulf Coast and shores worldwide since 1880. The database, called SURGEDAT, is unique in that it pulls from historical data to help validate computational modelling approaches to hurricane and storm surge predictions.“When we started this research in 2008, this approach was completely unique,” said ‘Hurricane’ Hal Needham, Geography and Anthropology graduate student at LSU and leading graduate researcher on the project. “Modeling is very useful, but you need to validate it with what’s happened historically. That is what we are trying to do here.”Historical observations as collected in SURGEDAT may help improve storm surge modelers’ forecasts of future storm surges and potential damages caused by high tropical storm waters. As tropical cyclone-generated storm surge is a complicated hazard and one that many coastline inhabitants and even emergency personnel don’t fully understand, the database can help citizens and officials better prepare for approaching storms and plan evacuations.bq. “SURGEDAT should hopefully help people understand their risk and plan ahead.” - Hal F. NeedhamThe SURGEDAT database is already providing new insights into storm surge climatology and where surges are most likely to occur.“When I started this research, I thought it was a crazy coincidence that the two biggest storm surge events we’ve seen – surges from Hurricane Camille in 1969 and Hurricane Katrina in 2005 – happened in the same location,” Needham said. “This gives support to the idea that there is a pattern here, that this isn’t random.”SURGEDAT currently provides an interactive map showing locations of more than 400 peak surge events along the Gulf Coast and worldwide. The coordinates for each surge event are plotted in a Geographic Information System, or GIS, with each surge event represented by a circle on the map. Larger, darker circles represent larger surges.For more about SURGEDAT, read the whole story on LSU’s website, written by LSU Research Communications Intern Paige Brown.SURGEDAT.jpgGraphical representation of SURGEDAT database.—NOAA Surge Vulnerability Facts:1. Much of the United States’ densely populated Atlantic and Gulf Coast coastlines lie less than 10 feet above mean sea level.2. Over half of the Nation’s economic productivity is located within coastal zones.3. 72% of ports, 27% of major roads, and 9% of rail lines within the Gulf Coast region are at or below 4 ft elevation (CCSP, SAP 4-7).4. A storm surge of 23 ft has the ability to inundate 67% of interstates, 57% of arterials, almost half of rail miles, 29 airports, and virtually all ports in the Gulf Coast area (CCSP SAP 4-7)

Have I lost trust with the National Trust? (from Brian Derby's blog)

Fri, 07/06/2012 - 6:07am

I read in the Guardian today that the National Trust’s new visitor centre at the Giant’s Causeway in Northern Ireland makes reference to Young Earth Creationism in its presentation on the geology of the formation. Now I understand that in Northern Ireland religion and politics are intertwined in a manner unfamilair to the rest of the United Kingdom; and that a protestant literalism interpretation of the bible is an important strand of opinion with a section of the community; however, I am dismayed that any organisation devoted to the maintaining of the landscape should pander to such an unscientific viewpoint.The National Trust tries to justify its stance with the following that I have copied directly from the Guardian article for those who cannot be bothered to follow the link.“The interpretation in the visitor centre showcases the science of how the stones were formed, the history of this special place and the stories of local characters.”We reflect, in a small part of the exhibition, that the Causeway played a role in the historic debate about the formation of the earth, and that for some people this debate continues today_.“The National Trust fully supports the scientific explanation for the creation of the stones 60 million years ago.”We would encourage people to come along, view the interpretation and judge for themselves_."_The interactive exhibition in question includes an audio package re-enacting debates between historic figures, who argued over the origins of the Causeway, as well as their contrasting biblical and scientific beliefs on the origins of the planet.The exchanges end with a further clip stating: "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 6,000 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_."This, to me, seems to be giving too much prominence to very unscientific theories and suggesting that they are hypotheses with validity that remain untested in the Popperian sense, which is clearly bunk. If the National Trust feels that balance is important, I hope that they give equal prominence to the hypothesis that the Causeway was built by Finn McCool (Fingal or Fionn mac Cumhaill in other traditions) trying to pick a fight with the Scottish Giant Bennandonner. This theory has as much evidence backin it as does the Young Earth theory beloved by creationists.

Higgs Excitement (from Brian Derby's blog)

Wed, 07/04/2012 - 7:54pm

After a years break from blogging the excitement of the Higgs announcement today has got me going again. The main effect of the announcemtnt that the higgs boson has been probably identified is a mushrooming of bad jokes built around the multiple meenings of the word mass. No, I won’t bore you with a poor selection of them. Judging by its influence on my teenage son, the discovery (possibly) of the Higgs has excited his interest in physics. Perhaps it is a pity it didn’t occur 6 months earlier as that might have improved his revision for his exams!I saw David Willets (Minister for Science) on Newsnight giving his opinion on the discovery – after having been flown out to Geneva for the occasion – he did not give a very good explanation of how mass was conferred by the Higgs field. He talked a lot about bosons bouncing off the particles and giving them mass.We should all (scientists that is) be grateful for the publicity that such occasional newsworthy articles on science generate. Understaning of the significance may not be universal but the generation of a sense of wonder about the natural world is to be welcomed.I can’t sign off without at least one flippant comment. I am not sure which of their songs would be appropriate for the occasion? Possibly “I’m the Urban Spaceman” but they could be (slightly) renamed the Boson God Doodah Band.

Fossils, Fun, and Frailities. And Statistics #isec2012 (from Bob O'Hara's blog)

Wed, 07/04/2012 - 10:45am

If I’ve done everything correctly, then at almost the moment this post appears, I will start talking about some fossils. Not, it’s not a eulogy about defenders of the 4-4-2 formation, but it’s about a bit of work I’ve been doing on trying to model when fossils appear and disappear. The work is still preliminary, in some ways, and it would be nice to get some feedback. So here are the slides:

Always look on the bright side (cartoon) (from Viktor Poor's blog)

Wed, 07/04/2012 - 8:33am

Science is a competitive sport. You might be at the finish line of your research, when an other research group publish those results.I guess, it happens at least once in every scientist’s life (if not you work on a too obscure topic and you won’t be able to publish your results). It happened to me last week, but always look on the bright side:look at the bright side.PNGCheck out this funny cartoon guide for a successful PhD entrance exam at Stripped Women in Science

Dinosaurs in the Wrangell Mountains (from Liz O'Connell's blog)

Tue, 07/03/2012 - 2:22pm

by Ned RozellThe more Tony Fiorillo explores Alaska, the more dinosaur tracks he finds on its lonely ridgetops. The latest examples are the stone footprints of two different dinosaurs near the tiny settlement of Chisana in the Wrangell Mountains.Fiorillo, a dinosaur hunter with the Museum of Nature and Science in Dallas, recently wrote of the foot impressions of a large plant-eater and small meat-eater in the science journal Cretaceous Research. Fiorillo is a yearly summer visitor to Alaska who seems to discover something exciting on every trip.His latest published find is based on his travel to the Wrangells in 2008 with Thomas Adams of San Antonio College, Yoshitsugu Kobayashi of Hokkaido University and Linda Stromquist of the National Park Service. Fiorillo had read about prehistoric plant fossils that others found in a streambed near Chisana. That type of vegetation in other places sometimes leads to dinosaur fossils.Dinosaur_FiorilloTeam.jpgFrom left, Yoshi Kobayashi, Tony Fiorillo and Tom Adams in the Wrangell Mountains near where they discovered dinosaur tracks. Photo courtesy Tony Fiorillo“That was the year there was no summer,” Fiorillo remembered of the rainy, cool 2008. “But for 12 days in the Wrangells, we had unbelievable weather. It may be the most beautiful field experience I’ve ever had.”Not long into the fieldwork, Fiorillo picked up a plate-size rock and held it up in the sunshine. He could see the impression of the middle toe of a three-toed dinosaur; by squinting at the rock as he turned it, he could make out a print pressed into the ground by a hefty creature that stomped past 70 million years ago. Close by, he recognized another print, the track of a smaller, zippy meat-eater.He called over his colleagues one by one and didn’t tell them a thing. Instead, he asked them what they saw. One spotted the plant-eater track right away; the other pointed out the meat-eater’s print. The moment marked the first official records of dinosaurs in Wrangell St. Elias National Park.Fiorillo described the two Wrangells dinosaurs: The larger one is a hadrosaur, a duck-billed dinosaur taller than most men and heavy as a car. The hadrosaur, similar to those that left tracks on Alaska’s North Slope and other areas of Alaska, ate plants, possibly the many ferns that also left their fossils behind in the area. Fiorillo envisions the Wrangells of 65 to 70 million years ago as a “fern prairie.”Dinosaur_HadrosaurTracks.jpgThe stone impression of tracks left by a hadrosaur in the Wrangell Mountains about 70 million years ago. Image courtesy Tony FiorilloThe second track is from a therapod (a group that includes, on the large end of the scale, T. rex). “This little guy ran around on two legs, might have been six feet from snout to tail and had a bunch of little pointy teeth and sharp claws,” Fiorillo said. “He was eating meat, but there was a lot of this ecosystem we didn’t pick up (fossils that would indicate what the dinosaur as tall as a kindergartner was eating).”With these finds, and more to be announced once the publishing cycle catches up with Fiorillo’s recent discoveries, Alaska in the time of the dinosaurs is coming into focus.“The Wrangells is a new area for dinosaurs, an area that looks very different from the North Slope and Denali (areas where similar dinosaurs lived),” Fiorillo said. “There’s this stereotype of Alaska being barren, of not much going on but people and other animals freezing all the time. But 70 million years ago, the ecosystem in the ancient high latitudes was biologically very productive.”Dinosaur_TherapodTracks.jpgThe stone impression of tracks left by a small meat-eating dinosaur in the Wrangell Mountains about 70 million years ago. Image courtesy Tony FiorilloSoon, Fiorillo will flee the blistering heat of Dallas for the breezy ridgelines of Alaska. This summer, he returns to both Denali National Park and a bend of the Colville River rich with the hardened remains of dinosaurs. Up north, he’ll search for clues as to how dinosaurs could have survived the darkness of winter, even though Alaska was as warm as Washington state millions of years ago. In Denali, he’ll continue exploring a rich area he started on last year, and try to flesh out a “completely bizarre” dinosaur he believes existed there..Check out Frontier Scientists projects on Arctic Archaeology, and join archaeologists in the field as they uncover a Paleo-Eskimo Camp.Since the late 1970s, the University of Alaska Fairbanks’ Geophysical Institute has provided this column free in cooperation with the UAF research community. Ned Rozell is a science writer for the Geophysical Institute.Originally posted at University of Alaska Fairbanks News: Headlines by Ned Rozell on June – 26 – 2012 http://www.uafnews.com/headlines/dinosaurs-in-the-wrangell-mountains

Lord of the Files, part 2 (from Peter Etchells' blog)

Tue, 07/03/2012 - 12:17pm

Back in November, I wrote about the Diederik Stapel affair that was rocking the psychological community. Now, it’s all happening again – recently, Uri Simonsohn has found evidence suggesting that another Dutch social psychologist, Dirk Smeesters, has been tinkering with data to produce more desirable outcomes in his research. We’re still waiting on Simonsohn’s paper on the matter to be published, so I think it’s a little too soon to speculate on how he came across Smeesters’ work – some have already started to make melodramatic comments likening Simonsohn’s approach to medieval torture. Clearly, we need to be very cautious about using such approaches as a sledgehammer. We don’t want to end up in a situation whereby completely innocent researchers wrongly getting caught out. But there are also some tough questions that need to be asked about how and why this sort of behaviour is happening. One thing that hasn’t been mentioned all that much in the media hype around both the Stapel and Smeesters cases is the collateral damage caused by their misconduct. Here’s what I wrote on the matter about the Stapel case in November:…I feel acutely sorry for the PhD students that Stapel, in supervising them in such an irresponsible way, has dragged through the mud. These students never got the chance to experience the full training that a PhD program is supposed to convey – they never got to run the experiments for themselves, to see how things go wrong, how to deal with setbacks. The few students or colleagues that did try to ask for access to the data were given excuses, and in some cases threatened or insulted. Gaining a PhD is a rite of passage in the academic world, and it’s nothing to do with getting some letters after your name or coming up with the next new game-changing theory. It’s about developing an inquiring mind, about gaining expertise incoming up with sensible, testable hypotheses and experiments, and learning how to accept that it’s okay when things don’t work. Sometimes a null result can be just as interesting as confirmation of a hypothesis.I think this still stands, and now seems to be compounded by this latest scandal. It looks like a few people who worked with Stapel also worked with Smeesters, and are now having to go through another round of papers being retracted and reputations being smeared. Some, like Jonathan Levav, have started to speak up in defence of themselves and their colleagues, and it’s clear that that emotions are (understandably) running high (it might also be worth watching Camille Johnson’s blog, another of Smeesters’ colleagues, in the coming weeks to hear her perspective on things). For any PhD students involved, this is going to be particularly painful. For one, it means they’ve been let down in their training – one of the most important things that I learned during my PhD was that world is a big noisy, messy place, and that’s okay. Data aren’t always neat and tidy; in fact neat data are the exception, not the rule. I worry that a number of students that have gone through these labs will spend a good chunk of their careers with the expectation that results need to be pristine in order to be meaningful, and that hurts both them and the science involved.Furthermore, the retractions could be potentially disasterous for their short-term career prospects. The pressure to publish is huge right now, and something that I myself am acutely aware of. Alongside the feeling of elation when a paper is published, there’s increasingly also the feeling of relief that it’s another one that you can add to your CV to make yourself look more employable. For Stapel and Smeesters’ students, having their work retracted will be an awful, awful blow. So yes, Psychology (and perhaps science in general, as it’s happening in other areas) needs to take a long hard look at how it’s got into this mess, and make amendments sooner rather than later. Funding bodies like the EPSRC are going to be plugging huge amounts of money into Doctoral Training Centres in the coming years, and with this influx of PhD students comes the duty to train them in appropriate, ethical, and sustainable research practices – otherwise, the same mistakes will just be made all over again.

Pot, Perspiration, Plant Photobiology and Pelage (from Lowell Goldsmith's blog)

Tue, 07/03/2012 - 8:00am

With Guest Blogger Julie S. Green, MD, PhD, University of Colorado Denver800px-Cannabis_sativa_leaf_Dorsal_aspect_2012_01_23_0830-by-JonRichfield-from-Wikipedia.JPGThe psychotropic properties of marijuana (MJ), prepared from the Cannabis sativa plant, have been appreciated for thousands of years. Nearly 50 years ago, delta-9-tetrahydrocannabinol (THC) was synthesized in the laboratory and was shown soon thereafter to be the primary active ingredient (Mechoulam et al, 1967; Mechoulam and Gaoni, 1967) in MJ. The relative proportion of THC to other, less active ingredients, determines the “potency” of MJ derived from a particular strain of C. sativa and generally averages a THC content of 2-3%, though some variants specifically bred for recreational use approach 20% (Pijlman, et al, 2005).Decades of research have associated the intake of THC (for example, via smoking MJ) with increased risk of anxiety and psychosis, the development of dependence and addiction, and appetite enhancement. THC produces these effects by binding two types of receptors found within the central nervous system and various peripheral tissues (including eccrine sweat glands). These receptors, designated CB1 and CB2, can be activated by THC, but they are also activated by endocannabinoids (ECS), compounds that are chemically related to THC but are naturally produced by the body. ECS are related to arachidonic acid, and they bind to CB1 or CB2 to modulate a number of physiological processes such as appetite, mood, and memory, so that the body does not need exogenous MJ (or ganja, mary jane, weed, or stuff ) for stimulation. An active area of current research involves studying the effects of stimulating or inhibiting the activity of these receptors. Both CB1 and CB2 receptors are present in eccrine sweat glands. Using a viral-transformed eccrine cell line Czifra et al recently studied the effect of ECS, which suppressed proliferation and increased apoptosis of sweat cells. Interestingly, the effect was not mediated by G proteins, which usually mediate CB2 receptor responses, but were mediated by the MAP Kinase pathway, which is active in some epidermal diseases. An unanswered question is whether there are influences, short or long-term, on eccrine sweating induced by exogenous THC in MJ users. This deserves at least taking detailed histories in dormitory rooms and coffee houses, and even direct measurement of eccrine sweat function in MJ users. Studies involving MJ administration would require institutional review board approval and approval by the US Drug Enforcement Agency (DEA). MJ plants (Cannabis sativa) synthesize cannabinoids and produce more active THC when exposed to increased levels of UVB (Lydon et al, 1987). That is why so many UVB light bulbs are used not for tanning but for C. sativa cultivation — and why C. sativa is often grown at high elevations. The US Department of Agriculture has carefully studied the UV effects, and Lydon et al. describe detailed techniques for growing C. sativa plants. Such information suggests ambivalence on the part of the US government towards MJ — or the misperception that plant growers do not use Pubmed and Google. The Sativa plant that produces MJ is a cultivar closely related to the sativa that produces hemp, a rather dull but commercially important product; plants in that family produce seeds that are an important oil and protein source (Pate, 1994). (The Journal of the Industrial Hemp Association, in which this report was published, had a brief life span, but discussions of the life and death of research journals is a topic for another day). While only this particular group of plants produce THC, it is unlikely that the plants use these chemicals for a high; nonetheless, the role of THC in plant ecology is uncertain. Insects do not have CB receptors, but THC may play a role in controlling competing plants, fungi and other parasites, and herbivores. THC also provides a modest sun protection factor, but sun protection is not a likely role for THC in sativa. Many are interested in knowing whether individuals are using — or have recently used - MJ. When I enter my local Lowe’s to buy tools for my silver workshop I always notice the sign announcing that drug testing is required for employees; that assures me the employee will lead me to the correct aisle to find an odd-sized file or drill bit. And this is where hair enters to story (Huestis, 2007). MJ is converted to polar and nonpolar metabolites, many of which enter growing hairs. There are sensitive analytical techniques for detecting THC, and hair is an archeological record of past MJ use. Incorporated THC cannot be removed by ordinary techniques available in the home or smoke-shop laboratory. Hair must be washed with lipid solvents to remove any environmental MJ contamination from the sample. There is always the possibility of sampling pubic hair to decrease the likelihood of contamination by ambient MJ, but that seems a bit intrusive. Plucked anagen hairs would allow a more timely analysis of recent MJ usage and would be a good research project for skin biologists.Since C. sativa and THC have been interacting with humans for millennia, studying ecology and the interface between plants and humankind is a legitimate reason to be growing sativa . . . register with the DEA, get permission to grow the plants, develop testable hypotheses, publish your results, and earn credibility as a sativa ecologist. You may make lots of friends in the process.REFERENCESHuestis, MA Cannabinoid Concentration in Hair from documented Cannabis users. Forensic Sci Int 169:129-136, 2007.Lydon J et al UV-B radiation effects … Photochemistry and Photobiology 46:201-206,1987.Pate, DW Chemical ecology of Cannabis. J International Hemp Assoc 2:29,32-37,1994.Pijlman FT, Rigter SM, Hoek J, Goldschmidt HM, Niesink RJ. Strong increase in total delta-THC in cannabis preparations sold in Dutch coffee shops. Addict Biol 10: 171-180, 2005.Mechoulam R and Gaoni Y. The absolute configuration of delta-1-tetrahydrocannabinol, the major active constituent of hashish. Tetrahedron Lett 12, 1109-1111, 1967.Mechoulam R, Braun P, and Gaoni Y. A stereospecific synthesis of ()-delta 1- and (-)-delta 1(6)-tetrahydrocannabinols. J Am Chem Soc 89: 4552-4554, 1967.TO COMMENT:

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Bad vibrations... Warier (from Lee Turnpenny's blog)

Mon, 07/02/2012 - 1:10pm

Further to my comments on the wonderful properties of Conception Flower and Gem Essence, I have spent some more time perusing the website, having still not received response to my query. Perhaps because it wasn’t received; or it might signify contempt towards someone who is clearly a time-wasting idiot, unable to navigate the site, wherein, at the very top of the page I reviewed, it states:bq. ‘If You are Struggling with Infertility Homeopathic Remedies Can Help’ and scrolling down, it clearly reads… bq. ‘(For more information about Flower and Gem Essences, please Click Here).’So I did. And my eye was immediately caught by:bq. ‘Discover the healing power in the vibrational energies of the selected flowers’‘Uh-oh,’ I thought. Although I guess that helps a bit, me having assumed (and we can’t have that, can we?) that the vibration came courtesy of the ‘gem essences’ alone. Well, skipping over the predictable and lazy appeal to authority that is the quoting and mini-synopsis of the career and maverick wacko ‘philosophy’ of one Edward Bach, we learn that:bq. ‘The philosophy behind the flower essences is that optimum physical health can only be achieved through emotional and spiritual harmony which will free the body of blockages and allow it to heal itself.’Each to their own; I find potatoes work very well, myself. So, why should it bother me whetherbq. ‘The healing effects of flower essences come from the vibrational energies of the selected flowers.’? Because I consider it utter bullshit? Or because I don’t know what it means? What are these ‘vibrational energies’? How do they connect with the ‘soul’ and ‘the emotional and spiritual body’? You see, I really don’t get, for example, howbq. ‘Holly heals anger and envy and therefore opens up the heart to allow the individual to be truly loving.’As in, get you ‘in the mood’ for conception? Is holly, then, an aphrodisiac?A quick reminder of the gem essences, which arebq. ‘… manufactured in a similar way to flower essences, but harness the vibrational energies unique to each different gemstone or crystal.’So, it is a physical extraction process? How, then, do you know you’ve captured them? Is there some sort of mass spectrometrical analysis of the extract to determine sufficient quantity of the purified ‘essence’? Is there quantification of its ‘vibrational energies’? And how do they work, specifically? Some kind of molecular massaging thing? However, let’s not over-concern ourselves with some tedious real science, when a good old dollop of bamboozlingly impressive pseudoscience will do just fine:bq. ‘According to quantum physics laws, when two objects vibrating at different frequencies are brought together, they impact on each other and an interference pattern is set up out of which a new frequency of vibration is produced.’Quantum physics, eh? Which, being too abstruse for physicists themselves to fully grasp, is sure to impress we lay suckers folk in its fuzziness. Although I didn’t realise that ‘interference patterns’ came under the moniker. But hey, I’m ever happy to be corrected. As I’d be happy to learn about the ‘frequency’ (singular) of a person. Do I read correctly from this, therefore, that when we feel unwell, our frequency drops? The higher our frequency, the healthier we are? That when we are feeling ‘high’ or feeling ‘low’, is it literally our individual frequency we describe? Anyway, going back to the clarification I had sought via the ‘ask us’ facility, as to whether this stuff is homeopathic or not. It turns out that:bq. ‘Flower and gem essences are a unique healing modality in their own right. They are different from herbal and homeopathic remedies.’Ah, is this the answer to my query? In contradiction of the previously apparent homeopathic remedy selling line, these are not the same thing. Moreover, their production prevents:bq. ‘… degeneration of the remedies and… any decrease in the healing vibrational energy of the flowers and gems from which they are made.’Would be very interesting to learn how they can preserve these ‘healing vibrational energies’, me supposing their production process is proprietary. But scroll down and we’re given insight… and another common natural fallacy selling point – all production and packaging is done by hand. Because – how silly not to have realised – any electronic/mechanical involvement couldbq. ‘… negatively affect the vibrational healing energy of the flowers or gems in any way.’Rrrrrright….? Well, presumably having gone to the trouble of conducting and/or referring to extensive research (details of which would, of course, clutter up the site and its readability, so let’s not over-concern ourselves with all that), it pays to take care with these ingredientsbq. ‘… in order to retain the full vibrational energy of the flowers and gems used.’Because these are very special essences indeed – coming, as they do, ‘from a Spiritual Place’.Do you, like me, form an impression of the people who are likely to be seduced by this ‘appeal to nature’ logically fallacious marketing? People who willingly buy that:bq. ‘NaturalEco Essences are completely hand-produced on the southern tip of Africa at the foot of Table Mountain, believed by many to be one of the twelve chakras of the planet Earth and a place where the energy leylines of Africa converge.’I’m not saying they are not produced there, from flowers ‘wild crafted or grown organically in the beautiful and tranquil Constantia hills away from noise, pollution and power lines which can all adversely affect the flowers and their healing properties.’ Although quite how the production process confers resilience to these adverse mechanical and electronic effects during subsequent transportation, storage and distribution, I fail to grasp. Particularly when we are reminded of the ’ sensitive nature of the vibrational energy’, which necessitates storage of ‘the essences far from any source of magnetic fields including electronic equipment.’ And I still struggle to understand how a ‘similar process’ of distillation in pure water works for gems as it does for flowers. And what of the luring in of the herbally and homeopathically gullible like tickled trout, only to inform them that these products ‘are different from herbal and homeopathic remedies’? (Not that I’ve sympathy, mind.)Just how many more examples can be squeezed onto this compendium cart of unclarities and contradictions? Well, here’s another to end with: bq. ‘Due to the manufacturing process, there are no side effects or drug interactions with Flower Essences and they are completely safe…’Which, then, I take to mean that there are *no* effects. Still, they do disclaim any guarantee that they work anyway. And a snip at $34.95 (Plus Shipping & Handling). Hardly worth making the effort to complain, eh?

Eating Urchins (from Graham Morehead's blog)

Fri, 06/29/2012 - 3:30pm
CITtedTalks4P062812.jpeg

<!-- Place this tag where you want the +1 button to render --> <!-- Place this tag where you want the StumbleUpon badge to render --> ')[NOTE: these postings have been rare of late due to thesis work]

Well, I tried out again for TEDx. It was covered in the local newspaper. Afterwards the audience voted. Again I did not win, but I had a great time. This time I focused a little more on my own research. This is basically what I said:

Strongylocentrotus drobachiensis is a spiny ball-shaped echinoderm we like to call the “Sea Urchin”. They’re like little sheep of the sea, going around mowing down the seaweed; real slowly, about zero miles an hour.

urchin-gonads.jpgPeople eat ‘em! If you turn one over you’ll see the little mouth with five chompers. Crack it open and you’ll find several globuous nodules, the gonads of the creature. Each one has the shape of a mushy slice of pear and tastes like rancid seawater, but people love them! and they’re willing to pay good money too.

So, we fished them, and we fished them hard. They used to be everywhere in the Gulf of Maine. They were all over the place … gettin’ all up in our lobster traps. Now they’re hard to find. The Maine Department of Marine Resources had to lower fishing limits again and again and again. In Casco Bay, if you want to harvest urchins, and you’re one of the lucky few who has a license, your fishing season is ten days a year. TEN DAYS! That’s it! You can’t be an urchin fisherman anymore. That’s not a profession you can have now. You’ve got to do something else.

Why are they so hard to find? We do surveys every year. We have an idea of how many are out there and we’re not taking too many. That’s not the problem. They problem is much harder. It’s actually been a mystery for a number of years.

I spent the last two years of my life on this problem. I wrote a computer simulation of the sea urchin ecology from the perspective of a nascent field of science called Complex Systems. A complex system is just a bunch of things that all interact with each other according to rules. Choose any two things from that system and you can understand their interaction precisely, but get a few million together and who knows? We can’t predict it or understand it intuitively. A classic example of a complex system is an economy. Nobody knows what our economy is going to do tomorrow.

fig7.jpgThere is a possibility that the output of my research may provide a new way to harvest sea urchins. We can take all the urchins we’re taking now, while simultaneously allowing the urchin populations to bounce back, with the promise that subsequent years will bring larger harvests even as those populations keep on increasing.

This August I will graduate and hand in my thesis, and I hope to have something to talk about. Thank you.

Risky Betting for Rating Mild Psoriasis Therapeutic Outcomes: Intra-Class Correlation Coefficients Confirm Low PASI Score Inter-rater Unreliability (from Lowell Goldsmith's blog)

Thu, 06/28/2012 - 10:00am

GUEST BLOGGERS:Robert P. Dellavalle and Julie GreenUniversity of Colorado DenverSolitare-Image-from-Flickr-by-sskennel.jpgIn 1946, the mathematician Stanisław Ulam wondered how many times a 52 card deck would play out successfully in a game of solitaire. Instead of mathematically calculating the solution Ulam empirically played the solitaire one hundred times and observed the results. And thus the Monte Carlo simulation (named after the popular European casino where Stanislaw’s uncle frequently gambled) was born.Monte Carlo simulations used in space and oil exploration, and many other risky endeavors, predict cost and schedule overruns. So a gambling moniker is appropriate. Increased computer power has made Monte Carlo simulations easier over the years since Ulam used them to help produce nuclear bombs during the Manhattan project. Monte Carlo simulations now model a boggling array of phenomena ranging from predicting the weather, determining the lifetime energy output of wind farms, forecasting the impact of pollution, optimizing winning strategies for games like Battleship and Go, modeling virtual 3D images, and valuing a company’s assets, to optimizing the design of wireless telephone networks.And why did we spend so much time on calculus in high school?Monte Carlo simulations are comprised of computational algorithms performed on multiple random samplings. In the recent JID paper by Gourraud and colleagues (Gourraud et al., 2012) the authors examined samplings of theoretical Psoriasis Area Severity Index (PASI) scores.The PASI was developed to standardize assessment of the severity of psoriasis and changes in severity over time in individual patients. The PASI reflects a mathematical equation that incorporates scaled measurements of psoriasis-related erythema, induration, and scaling on the head, arms, trunk, and legs, which results in a score that ranges from 0 (no disease) to 72 (maximal disease). Because two clinicians evaluating the same patient rarely calculate the same PASI scores, these measurements are at least partially subjective. The PASI scoring system is also too cumbersome for many clinicians to incorporate into daily practice.Many clinical research protocols have used the PASI scoring system to monitor responses of patients to experimental psoriasis treatments, and determination of efficacy is generally based upon the FDA guideline of at least a 75% improvement in PASI score. Using the Intra-Class Correlation Coefficient (ICC) Gourraud and colleagues confirmed what has long been suspected but hidden by less appropriate statistical methods—that for patients with limited psoriasis (evidenced PASI scores below 20) PASI scores are not reliable measures of therapeutic outcome. These results confirm the need for better therapeutic outcome measures of psoriasis for patients with limited psoriasis (Jensen et al. 2010).References:Jensen JD, Fujita M, Dellavalle RP. Validation of Psoriasis Clinical Severity and Outcome Measures: Searching for a Gold Standard. Commentary on: How Good Are Clinical Severity and Outcome Measures for Psoriasis?: Quantitative Evaluation in a Systematic Review by Spuls PI, et al. Arch Dermatol, 2011 Jan;147(1):95-8. PMID: 20855674.Gourraud, P-A, Le Gall C, Puzenat E (2012) Why Statistics Matter: Limited Inter-Rater Agreement Prevents Using Psoriasis Area and Severity Index as a Unique Determinant of Therapeutic Decision in Psoriasis. J Invest Dermatol epublished 17 May 2012.Wikipedia, Stanisław Ulam Accessed June 2012This image was obtained from Flickr, and it is by sskennel.

Update on Miami 'face eater' and Bath Salts (from Suzi Gage's blog)

Thu, 06/28/2012 - 7:08am

Sorry for the silence on the blog recently, a combination of gigs in exciting locations (Odessa sea front), conferences practically in the Arctic Circle (Oulu – blog on that to come) and hiding in Cornwall to write some papers have meant I haven’t had a moment, but…I’ve just seen that the toxicology report came back on Tuesday for Rudy Eugene, the man shot dead by police while chewing another man’s face on the side of the causeway.Initially a drug called bath salts was blamed, and I wrote a blog about the drug, also commenting that there was as yet no evidence he had taken anything at all.And so back to the toxicology report. According to reports in The Guardian and The Huffington Post, none of the chemicals usually present in bath salts were found during the toxicology tests. In fact, the only drug found in his body was cannabis (I assume this means they found delta-9-THC – the active component of cannabis, but I can’t find anywhere that reports this).This quote was taken from the Guardian, who were quoting a press release from the Medical Examiner’s office:"The laboratory has tested for but not detected any other street drugs, alcohol or prescription drugs, or any adulterants found in street drugs. This includes cocaine, LSD, amphetamines (ecstasy, meth and others), phencyclidine (PCP or “angel dust”), heroin, oxycodone, Xanax, synthetic marijuana (“spice”), and many other similar compounds.“So it doesn’t sound like it was ‘bath salts madness’ then – but could cannabis cause this kind of extreme reaction? Well, there is evidence from a randomised controlled trial that delta-9-THC intoxication can transiently induce the positive symptoms of schizophrenia, namely paranoia, grandiose delusions, hallucinations and depersonalisation (see ”http://www.ncbi.nlm.nih.gov/pubmed/15173844">D’Souza et al, 2004 for the trial).However, seeing things or feeling paranoid isn’t quite the same as what happened in Miami, so once again, I think it’s likely to be a little more complicated than a drug causing a reaction.I’d love to hear your thoughts on this development to the story!

Trees, grass and carbon dioxide and the battle for dominance (from Grrl Scientist's blog)

Thu, 06/28/2012 - 5:00am

SUMMARY: A new study shows that increasing carbon dioxide levels favours trees over grass, suggesting that large regions of Africa’s savannas may be forests by the end of this centuryAfrican savanna.
Image: Steve Higgins [doi:10.1038/nature11238].The African savannas appear peaceful but beneath the wings of birds and the hooves of mammals, a millennia-long battle is being fought. This struggle determines whether vast regions of the tropics and subtropics are covered in grasslands, savannas or forests. But a new study shows that rising concentrations of CO2 are shifting the odds to favour trees over grasses, suggesting that large regions of Africa’s savannas may be forests by the end of this century.