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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:TweetCheck out this funny cartoon guide for a successful PhD entrance exam at Stripped Women in Science

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.From 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.”The 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.”The 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

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.

With Guest Blogger Julie S. Green, MD, PhD, University of Colorado DenverThe 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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The image is used under the Creative Commons Attribution-Share Alike 30 Unported license. The image can be found at Wikipedia and is attributed to JonRichfield

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?

<!-- 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.

People 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.

There 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.

GUEST BLOGGERS:Robert P. Dellavalle and Julie GreenUniversity of Colorado DenverIn 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.

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!

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.

Methane-induced melt-hole on a frozen lake in the Brooks Range in Alaska in April of 2011. Photo by Katey Walter Anthonyby Marmian GrimesGeologic methane is seeping through the edges of thawing permafrost and receding glaciers in Alaska and Greenland, according to a study recently published in the journal Nature Geoscience.University of Alaska Fairbanks researcher Katey Walter Anthony led the study, which, for the first time, documents the widespread occurrence of these terrestrial sources of geologic methane seepage in the Arctic.“They had never before been quantified and we didn’t know they were so widespread,” she said.In the past, researchers have found that, as permafrost thaws, previously frozen organic matter like dead plants or animals decays and releases methane.“Now we are saying that as permafrost thaws and glaciers retreat it is going to let something out that has had a lid on it,” Walter Anthony said.In the Arctic, that lid is known as the “cryosphere cap.” It’s made up of glaciers, permafrost and ice sheets, which are thought to keep geologic sources of methane—such as coal beds and natural gas deposits—from venting into the atmosphere. However, as permafrost thaws and glaciers retreat, this cap can develop leaks, allowing the methane to escape.Walter Anthony and her team saw this manifested in Alaska and Greenland lakes, where rapidly rising methane plumes created patches of open water in otherwise frozen bodies of water. In order to quantify the phenomenon, the researches flew across the state of Alaska, from the Kenai Peninsula to the North Slope, during the winters of 2008 through 2010, and hiked across lakes in Greenland during the winter of 2010. They surveyed nearly 7,000 lakes from the air and identified 77 of them that were very likely to have sites where methane was seeping. Then, the scientists visited 50 of the lakes to confirm the presence of seeps and take samples of the gas boiling up from under the water. They later tested the samples and determined the gas’s source was geologic, rather than the result of decaying organic material. The majority of the seeps were in the continuous permafrost zone in northern Alaska and in Southcentral Alaska, where glaciers were receding. In Greenland, the seeps were found only in the areas where the ice sheet had retreated during the past 150 years.Methane is important in the global climate picture because it is a potent greenhouse gas. It is more than 20 times more effective at trapping atmospheric heat than carbon dioxide.Walter Anthony said that according to the data from this study, geologic methane seeps in Alaska’s terrestrial environment may contribute about 250,000 metric tons of methane to the atmosphere each year. In comparison, Walter Anthony estimates that organic decay in Alaska’s lake bottoms contributes about three times that amount. However, she noted that those numbers don’t include microseeps of geologic methane, which could mean geologic sources roughly equal the organic sources.“When the glaciers retreat or the permafrost thaws,” she said, “it creates conduits for deeper gas to make its way up through the Earth.”And those conduits could become more widespread if worldwide temperatures continue to increase, Walter Anthony notes. “In a warmer world, thawing permafrost and wastage of glaciers and ice sheets could lead to a significant transitional degassing of subcap methane.”Co-authors on the paper include Peter Anthony and Guido Grosse, also of UAF, and Jeffrey Chanton of Florida State University.NOTES: To download additional photos, the audioconference recording and a video, visit our FTP site at ftp://cinema.wfb.uaf.edu. Cutlines are available in the multimedia guide.Username: uafnewsPassword: multimediaFolder: UAFmultimediaOriginally posted at University of Alaska Fairbanks News: Headlines by Marmian Grimes on May – 21 – 2012 http://www.uafnews.com/headlines/study-geologic-methane-seeping-from-thawing-cryosphereFind more on Permafrost and Arctic Climate Change at Frontier Scientists.

GUEST BLOGGERS:Jason Chouake, Albert Einstein College of MedicineDavid Schairer, Albert Einstein College of MedicineAdam Friedman, MD, Albert Einstein College of MedicineAdnan Nasir, MD, PhD University of North Carolina at Chapel HillThe Nanodermatology Society (NDS) recently held its first meeting in conjunction with the annual meeting of the Society for Investigative Dermatology in Raleigh, North Carolina. Scientists from around the globe met in person to present their research, discuss potential future collaborations, and integrate their knowledge. From the nine presentations, three major themes emerged: nanoscale delivery systems, application of nanotechnology in scientific development and research, and safety of nanotechnology.The development of nanodelivery systems is a hot area of nanotechnology research. Areas of interest range from nanoparticle platforms that can be used for enhanced wound healing or antimicrobial effects to the development of nanoneedles for drug and vaccine delivery. Two new nanoparticle platforms were presented that show the potential for nanotechnology in wound healing. Dr. Meya Li, from Menicon Co., reviewed data on self assembling peptide hydrogels , demonstrating their potential as a carrier of activating or inhibiting factors of wound healing. David Schairer, a dermatology research fellow from the Albert Einstein College of Medicine, showed how nanoparticles could be used to encapsulate, protect and deliver siRNA to promote accelerated wound healing. Harnessing nanotechnology to develop new antimicrobial agents was also highlighted. Jason Chouake, a dermatology research fellow from the Albert Einstein College of Medicine, reviewed his work using N-acetyl-cysteine-nitric oxide nanoparticles to combat virulent gram positive and negative bacterial species. In line with the role of nanotechnology in the management of infectious diseases, Dr. Geza Erdos, from the University of Pittsburgh, discussed how dissoluble microneedle arrays can be used to deliver activated cargo, such as vaccines, to targeted layers of the skin. Nanotechnology also enables more efficient and sensitive analysis of genes, and these techniques are already being used to characterize the association between specific genes and diseases. Dr. James T. Elder, from the University of Michigan, discussed how gene chips make it possible to identify infrequent or low risk alleles for psoriasis. It is now possible to test cohorts of up to 30,000 patients and thus obtain the statistical strength to identify these previously elusive alleles. Dr. Elder’s work is already being used by other researchers, like Dr. Antonio Costanzo from the University of Rome. Dr. Costanzo uses nanotechnology in the form of next generation sequencing technology coupled with chromatin immunoprecipitation (Nano-ChIP-seq) to explore the pathogenesis of psoriasis. Nano-ChIP-seq provides 2-3 order of magnitude improvement over conventional ChIP-seq in terms of the number of cells required to generate significant results. Using Nano-ChIP-seq, Dr. Costanzo and his colleagues have shown that IKKα is downregulated in patients with psoriasis, and they have discovered a novel nuclear function of IKKα as a repressor of inflammatory genes in keratinocytes. Both of these researchers highlighted how they capitalize on both the cost saving and data enhancing benefits nanotechnology confers to gene chips.In light of statements made by the FDA concerning the importance of characterizing the safety of new nanotechnologies for consumer use, Nancy Monteiro-Riviere discussed her work in the toxicological assessment of different nanoparticle platforms. She discussed how standards are slowly being developed to assess the safety of emerging nanotechnologies. When asked whether nanoparticle safety could be evaluated by particle class, Dr. Monteiro Riviere replied, “Each nanoparticle is different and the manufacturing processes as well as the particle itself are important factors that determine the potential toxicity of nanoparticles.” Dr. Monteiro Riviere argued that toxicity assays must be carefully selected, and that one assay is not sufficient to characterize the toxicity of a nanoparticle. Nanotechnology is being utilized and researched worldwide, and it will continue to be a major target of investigation by both private corporations and academic researchers. The collaboration between industry and academia through the Nanodermatology Society offers great potential for both translational and basic research collaborations. The NDS is a forum where scientists from different countries and settings can meet and develop relationships that involve exchanges among researchers in a field where geography and scientific research have no barriers, providing greater chances of success. In the words of Charles Darwin:In the long history of humankind (and animal kind, too) those who learned to collaborate and improvise most effectively have prevailed.To find out more about nanodermatology, we recommend the following resources:

1. DeLouise LA. Applications of Nanotechnology in Dermatology. J Invest Dermatol. 2012;132(3):964-975.
2. Blecher K, Nasir A, Friedman A. The growing role of nanotechnology in combating infectious disease. Virulence. 2011;2(5):395-401.
3. Nasir, A, Wang S, and Friedman A. The Emerging Role of Nanotechnology in Sunprotection: An Update. Expert Review Dermatol. 2011; 6(5): 437-439
4. Nasir A. Nanotechnology and dermatology: Part I-potential of nanotechnology. Clinics in Dermatology. 2010;28(4):458-66.
5. Nasir A. Nanotechnology and dermatology: Part II-risks of nanotechnology. Clinics in Dermatology. 2010;28(5):581-
6. Hia J, Nasir A. Photonanodermatology: the interface of photobiology, dermatology and nanotechnology. Photodermatology Photoimmunology & Photomedicine. 2011;27(1):2-9.
7. Nasir A, Friedman A. Nanotechnology and the Nanodermatology Society. Journal of Drugs in Dermatology. 2010;9(7):879-882.
8. Sandoval B. Perspectives on FDA’s Regulation of Nanotechnology: Emerging Challenges and Potential Solutions. Comprehensive Reviews in Food Science and Food Safety. 2009;8(4):375-393.

To learn more about the nanodermatology society, please visit our website: www.nanodermsociety.orgTO COMMENT:

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Can anyone tell me what is probably so famous about this site, in Essex? The bit of historical interest is next to the houseboat in the centre of the image.
View Larger MapIf you’re on twitter, or have read the right blogs, you know already. So no giving it away. And googling it is cheating. :-)And bonus points will be given for explaining the rectangles.

Following on from Tom’s recent Interlude, I thought I’d share some photos I managed to snap yesterday, as I was being attacked by wildlife.I had just arrived at the front gate with my family after an evening stroll, when my wife noticed someone complaining on the roof of the house across the street from us. I dashed upstairs to grab a camera before she (the focal species, not my wife) was mobbed and driven off by the angry local passerines and managed to snap her in this graceful pose.Are you talkin’ to me?I ran back upstairs to our balcony to try and get a better view, which apparently attracted the bird’s attention,Well I’m the only one hereI had to duck and cover before my face was grabbed in those uncomfortably sharp talons, and spent the next 20 minutes or so in a staring competition with this little beauty.Go on, blink. I dares yaShe tried hard to get in through the balcony doors, but had to be content with perching on the rail, growling at me.I can sit here all night. You’ve got to go and make supper.I’m still not sure if she was protecting her nest, I tried to look at our roof earlier this morning, but couldn’t see anything (not easy from street level), or protecting her prey – a dead sparrow lying in the tiles just below our balcony. I was glad to spend a bit of time with her though.So, at the risk of stepping on Grrrl’s toes, any guesses for the species?

Managing the amount of energy from the sun that enters our planet’s atmosphere may well be the only saving grace we have left from global warming. But that doesn’t mean that what researchers call solar radiation management is any less controversial in scientific and public spheres.Tweetbq. The Sun provides the energy that drives Earth’s climate, but not all of the energy that reaches the top of the atmosphere finds its way to the surface. That’s because aerosols—and clouds seeded by them—reflect about a quarter of the Sun’s energy back to space. (NASA)I first heard David Keith speak about geoengineering during ‘The Science of Science Communication’ #Sackler conference held this May in Washington, D.C. (I wasn’t actually in D.C., but watched the live webcast! Very handy…) David Keith, Gordon McKay Professor of Applied Physics at Harvard University and geoengineering expert, has been listed as one of TIME magazine’s Heroes of the Environment 2009 (article involves large-scale engineering and manipulation of Earth’s environment (Royal Society). Solar radiation management, a unique type of geoengineering, is all about adjusting the amount of sunlight that the Earth absorbs. Turning the dial down on sunlight could potentially offset climatic changes that are occurring as greenhouse gases like carbon dioxide increase in our atmosphere. Critics of solar radiation management often object to geoengineering on the principle of distraction away from true mitigation efforts. In other words, critics worry that in taking efforts to turn down the dial on sunlight, we will forget to fix the source of the problem: overproduction of greenhouse gases. But as David Keith said during a recent ScienceLive event, “Mitigation means reducing the amount of carbon we put into the atmosphere. In the long run, putting carbon to the atmosphere increases climate risk. There’s no getting away from that even with SRM [solar radiation management].” According to Keith, geoengineering CAN NOT save the world, but it may be an option to take seriously, as global temperatures will continue to rise long after we take significant measures to cut carbon dioxide emissions – if indeed we succeed at that before irreversible planetary changes occur.One option proposed to ‘turn down the dial’ on sunlight involves ejecting sulfate aerosols into the atmosphere. This occurs naturally, for example, when volcanoes erupt and spew ash and sulfate aerosol-generating gases into the lower atmosphere. Traditionally thought of as air pollution, the ejection of sulfate aerosols may actually cause the atmosphere to absorb less energy from the sun. Think of artificial clouds, like the ones in this picture I look of the Raleigh-Durham airport here in the U.S. (very pretty airport indeed). If we can create more artificial clouds to block out sunlight, we may be able to slow down Earth’s currently staggering rate of global warming. Could artificial clouds help protect our planet from the impacts of intense global warming?According to NASA: “Aerosols play an important role in Earth’s climate. Most aerosols are brighter than land or ocean, and cool the Earth by reflecting sunlight back to space.” So what would it take to see solar radiation management deployed as a way of saving Earth’s environment from the damaging effects of extremely warm global temperatures? I interviewed David Keith for this week’s From The Lab Bench blog post on geoengineering.1) Can you describe the lay of the land (briefly) of current climate change mitigation research, and where (solar) geoengineering currently stands as an effective mitigative option? What are some of the promises AND potential pitfalls of geoengineering.For me, mitigation means reducing emissions. Solar geoengineering, or SRM, is an entirely different option as distinct from mitigation as is adaptation. This usage of the term ‘geoengineering’ is standard but not universal in climate policy.Mitigation research should focus on finding low-cost large-scale ways to cut emissions of carbon dioxide from the energy sector. This means research into new low-carbon energy sources and the policy measures to drive their diffusion in a cost-effective manner. Globally, there is a lot of effort in this area. Bloomberg estimates that worldwide investment in “clean energy” has risen steadily to $260billion in 2011 – that’s 0.4% of world Gross domestic product (GDP) (http://bloom.bg/yK10VN). But this investment does not seem to be effectively focused on low-cost high impact measures, and emissions continue to increase rapidly.Solar geoengineering offers the potential to substantially reduce climate impacts over the next half century. At present, relatively little research has been done, so one cannot confidently say how effective SRM might be. But the reasons to take it seriously are simple: basic physics along with every climate model in which it has been tested suggest that SRM could substantially reduce the rates of climate change – not just the rate of temperature change but also the rates of change of other climate variables such as precipitation. It is therefore likely that it could substantially reduce climate change impacts.SRM is fast, cheap and imperfect. It entails significant risks. At present I think there is a very strong case for a substantial global research program given (a) the scale of the potential benefits, and (b) the fact that early evidence suggests that both the costs and risks are comparably small. 2) What is your take on public opinion of serious climate change mitigative action and geoengineering in particular? What do you think are the key aspects to improving public approval of mitigative policies and geoengineering options?Few people in the general public have strong opinions about these technologies. People’s opinions are not set in stone but rather depend on the way the issue evolves in the public arena. Early evidence suggests that a significant fraction of population in North America and the UK is in support of research on SRM, although this is by no means conclusive and it clearly depends on the way the question is asked (for an academic article on public perception see http://iopscience.iop.org/1748-9326/6/4/044006/) 3) Tell me more about solar geoengineering, and some of the most up-to-date research on solar engineering. What do you think are some of the long-term consequences (both good and bad) of pursuing this option for climate change mitigation?The central positive consequence of pursuing this option is that it could materially reduce climate risks for people and the natural world.In my view, the central risks are political, not technical. Put simply, our species lacks effective tools to manage the technology that gives us such large leverage over our Earth’s climate. The ability to manage climate could increase as well as decrease international tensions and might lead to an overemphasis on SRM without the appropriate efforts to reduce emissions. 4) What are the 3-5 most important things that the public should know about solar geoengineering, in order to inform their decisions on potential future geoengnineering policies?1. We cannot improve our understanding of the way these technologies work, of their risks and potential benefits, without a substantial research program. That program could be tiny (less than 1%) compared to the cost clean energy research, but a program that starts out at the least at a few tens of millions of dollars a year globally makes sense. If early results are promising, the program will need to ramp up from there.2. No kind of SRM can eliminate long-term climate risks unless we cut emissions of carbon dioxide towards zero.3. In concert with a technical research program, there is a need to develop methods of managing technology like SRM, with public as well as political and scientific expert input.Thank you David Keith.What questions do you have about geoengineering? —-References:1) Earth Observatory, NASA, on Aerosols: http://earthobservatory.nasa.gov/Features/Aerosols/printall.php2) Image: Image Science and Analysis Laboratory, NASA-Johnson Space Center. “The Gateway to Astronaut Photography of Earth.” <http://eol.jsc.nasa.gov/scripts/sseop/photo.pl?mission=ISS024&roll=E&frame=15122>06/24/2012 04:18:59.David Keith (1992). A serious look at geoengineering Transactions, American Geophysical DOI: 10.1029/91EO00231

Llamas!
(Llama glama)

Llamas could be the clue to finding a vaccine for HIV/AIDS, according to virologists at University College London. By harnessing a peculiar quirk in the llama immune system, the researchers were able to generate a special antibody that broadly neutralized the most common HIV strains known to man.

     HIV infects a cell by using a special “key” that coats the virus, called “envelope protein”. In defense, humans will produce antibodies that stick to the grooves of these keys, so they will no longer fit into their “locks”: receptor proteins on the cell surface (Video 1). 

However, HIV can dodge this shield by rapidly mutating its keys, so that neutralizing antibodies fail to recognize them. HIV’s high mutation rate explains why numerous strains exist worldwide (Fig. 1) and why this virus is so hard to treat. To be truly protected from HIV, a person must be vaccinated against the entire catalog (or at least a majority) of strains, or reinfection will always be a possibility.  

     All camelids- llamas, camels, alpacas – are unique in that they produce “nanobodies”, which are diminutive versions of regular, disease-fighting
antibodies. While a stereotypical antibody is comprised of “heavy” and “light”
chains of protein, a llama nanobody only has “heavy” chains (Fig. 3).Llamas To The RescueFig. 3. Antibody vs. NanobodyUpper Panel.  Antibody Chains:

Heavy (blue) & Light (pink) 

Lower Panel.  Antibody vs. Llama Nanobody
Because of their smaller stature, the scientists reasoned that nanobodies could squeeze into the harder-to-reach grooves of HIV’s key, with the hope that one of these interactions would be broadly conserved across HIVstrains.  Their hunch was right.
Two llamas were periodically inoculated - about once a week - with HIV envelope protein* (not the whole virus). Every 2 weeks, their blood was screened for antibodies. The researchers repeated this process until they eventually stumbled upon nanobodies that are powerful inhibitors of HIV infection, a finding that was initially reported in 2008. This was the first HIV neutralizing antibody found in a nonprimate. 
Llama Nanobody 2.0 &
Preventions for the Future.In their latest publication, the researchers isolated a new llama nanobody – named “J3” – that could neutralize 96 out of 100 of the most common HIV strains. The J3 nanobody shared structural features with neutralizing antibodies that were recently found in HIV-infected humans. Interestingly, J3 nanobody outperformed its human counterparts in this study.   
      Along with inhibiting a larger profile of HIV strains, J3 neutralized strains that could dodge antibodies derived from HIV-infected patients. It’s widely believed that antibodies can be adapted into vaginal microbiocides to reduce the spread of HIV. Unfortunately, microbiocides are temporary remedies, which must be reapplied on a regular basis to be effective. A vaccine that provides long-term protection would be more ideal, and llamas can help us find one. By studying how HIV envelope protein elicits the production of J3 and other nanobodies in llamas, researchers can gain insights on how to recapitulate the process in humans.
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BloggerGeek NotesNanobodies… I
cheated here and skipped a detail. Llamas make “single-domain antibodies” that lack light chains. A nanobody is fragment of this single domain antibody - the tip of the antibody known as the variable region (“VHH”, Fig. 4) - and is what would be used for clinical applications. As shown in Fig. 3, the VHH contains the regions that bind to antigens, like HIV’s envelope protein. Fig. 4.
just the HIV envelope protein… for the HIV experts, as an immunogen,
the authors used a gp140 trimers derived from the CRF strain CN54 (subtype BC) and the subtype A strain 92UG037.
Main CitationsFirst Study

Forsman A, Beirnaert E, Aasa-Chapman MM, Hoorelbeke B, Hijazi K, Koh W, Tack V,
Szynol A, Kelly C, McKnight A, Verrips T, de Haard H, & Weiss RA  (2008). Llama antibody fragments with cross-subtype human  immunodeficiency virus type 1 (HIV-1)-neutralizing properties and high affinity for HIV-1 gp120. Journal of virology, 82 (24), 12069-81 PMID: 18842738
Latest StudiesMcCoy LE, Quigley AF, Strokappe NM, Bulmer-Thomas B, Seaman MS, Mortier D, Rutten L, Chander N, Edwards CJ, Ketteler R, Davis D, Verrips T, & Weiss RA (2012). Potent and broad neutralization of HIV-1 by a llama antibody elicited by immunization. The Journal of experimental medicine, 209 (6), 1091-103 PMID: 22641382

Strokappe N, Szynol A, Aasa-Chapman M, Gorlani A, Forsman Quigley A, Hulsik DL, Chen L, Weiss R, de Haard H, & Verrips T (2012). Llama antibody fragments recognizing various epitopes of the CD4bs neutralize a broad range of HIV-1 subtypes A, B and C. PloS one, 7 (3) PMID: 22438910

Related CitationsLlama Nanobodies As MicrobiocidesGorlani A, Brouwers J, McConville C, van der Bijl P, Malcolm K, Augustijns P, Quigley AF, Weiss R, De Haard H, & Verrips T (2012). Llama antibody fragments have good potential for application as HIV type 1 topical microbicides. AIDS research and human retroviruses, 28 (2), 198-205 PMID: 21864083

Review On The Impact Human-derived Neutralization Antibodies
Burton DR, & Weiss RA (2010). AIDS/HIV. A boost for HIV vaccine design. Science (New York, N.Y.), 329 (5993), 770-3 PMID: 20705840

Neutralizing Antibodies Found In HIV Patients
Walker LM, Phogat SK, Chan-Hui PY, Wagner D, Phung P, Goss JL, Wrin T, Simek MD, Fling S, Mitcham JL, Lehrman JK, Priddy FH, Olsen OA, Frey SM, Hammond PW, Protocol G Principal Investigators, Kaminsky S, Zamb T, Moyle M, Koff WC, Poignard P, & Burton DR (2009). Broad and potent neutralizing antibodies from an African donor reveal a new HIV-1 vaccine target. Science (New York, N.Y.), 326 (5950), 285-9 PMID: 19729618 

Walker LM, Huber M, Doores KJ, Falkowska E, Pejchal R, Julien JP, Wang SK, Ramos A, Chan-Hui PY, Moyle M, Mitcham JL, Hammond PW, Olsen OA, Phung P, Fling S, Wong CH, Phogat S, Wrin T, Simek MD, Protocol G Principal Investigators, Koff WC, Wilson IA, Burton DR, & Poignard P (2011). Broad neutralization coverage of HIV by multiple highly potent antibodies. Nature, 477 (7365), 466-70 PMID: 21849977
Wu X, Yang ZY, Li Y, Hogerkorp CM, Schief WR, Seaman MS, Zhou T, Schmidt SD, Wu L, Xu L, Longo NS, McKee K, O’Dell S, Louder MK, Wycuff DL, Feng Y, Nason M, Doria-Rose N, Connors M, Kwong PD, Roederer M, Wyatt RT, Nabel GJ, & Mascola JR (2010). Rational design of envelope identifies broadly neutralizing human monoclonal antibodies to HIV-1. Science (New York, N.Y.), 329 (5993), 856-61 PMID: 20616233

Scheid JF, Mouquet H, Ueberheide B, Diskin R, Klein F, Oliveira TY, Pietzsch J, Fenyo D, Abadir A, Velinzon K, Hurley A, Myung S, Boulad F, Poignard P, Burton DR, Pereyra F, Ho DD, Walker BD, Seaman MS, Bjorkman PJ, Chait BT, & Nussenzweig MC (2011). Sequence and structural convergence of broad and potent HIV antibodies that mimic CD4 binding. Science (New York, N.Y.), 333 (6049), 1633-7 PMID: 21764753
Figure Sources
Video 1.http://www.hivinfosource.org/hivis/hivbasics/animations/index.html
Fig. 2.http://www.avert.org/media/content/graphs/subtypes.jpghttp://www.pbs.org/wgbh/pages/frontline/aids/art/clademap.gifhttp://www.hiv.lanl.gov/content/sequence/HIV/CRFs/CRFs.html
Fig. 3http://www.biology.arizona.edu/immunology/tutorials/antibody/prob_set/01t.htmlhttp://www.biotechniques.com/news/Nanobodies-Going-single-domain/biotechniques-257771.html
Fig. 4http://www.structuralbiology.be/chaperones

On Fridays I usually try to put up trivial amusing stuff. So please take this is that spirit, because you really don’t want to take this seriously.Encouraging women into science has to be a good thing, and there are good ways of doing it. But then there’s this:

My talk from the Sound Software 2012 workshop at Queen Mary University of London on Monday 18th – talking with domain-specific software experts about the scholarly record and how they might apply their sound software thinking to the greater challenge of reconstructable research.Different research communities have their own practices with respect to sharing and publishing research results, data, methods and software. The Music Information Retrieval (MIR) Research community is, I believe, an excellent example – particularly due to MIREX, the “Music Information Retrieval Evaluation Exchange” which generates an annual cycle of innovation and evaluation of feature extraction algorithms (this is not a competition, though it publishes league tables!) MIR researchers bring together digital audio collections (not freely copyable, so they send code to data), human-sourced “ground truth”, deep multidisciplinary expertise, software, algorithms, results and papers (in the ISMIR conference), and evaluations (in MIREX). It’s a significant and impressive sociotechnical infrastructure, owing something to information retrieval but reinvented as multimedia, multidisciplinary and, well, music.Let’s think about the scholarly communication perspective – the research record, which enables researchers to move forward standing on each other’s research shoulders. Conducting a music information retrieval experiment involves a set of digital artefacts which can be reused. For example in the SALAMI (Structural Analysis of Large Amounts of Music Information) project we have digital audio (from the Internet Archive), software tools (e.g. Queen Mary’s Sonic Visualiser), ground-truth annotations (published), segmentation ontology (published), algorithms (from MIREX), autocorrelation plots and evaluations (online). The record of a particular experiment, then, can be captured as an assembly of these artefacts. Just now we share some of the pieces quite well but perhaps not the aggregations.Typically an MIR experiment also involves an assembly of software apparatus – from a range of toolkits, with overlapping functionalities, each co-evolved for particular uses and sustained by their user and developer communities. The assembly is made particularly explicit where a workflow system is used, as in the flows of the Meandre system. There are multiple levels of abstraction: experts innovate in the algorithms embedded in specific components but also in their assembly into music analysis pipelines, whether using software, workflows or scripts. Such an assembly of software apparatus is rather like a scientific instrument – a datascope, taking us from signal to understanding – and itself under continuous improvement.While the world is now grasping the importance of data sharing, we must also grasp the importance of sharing these experiments and instruments; i.e. it’s not just the data, it’s what you do with it. Sharing builds community capability and better science, and this is what we want from the scholarly record. The sound software and MIR community is good at this, for example through software repositories, online resources and proceedings, and getting even better. Can we take this further?We have an angle on this based on experience with the myExperiment social website for sharing workflows and the associated Wf4Ever preservation project. We’ve learned that what people want to share isn’t just the workflow but the associated artefacts – slides, papers, data – and this has enabled us to reflect on the assemblies to be shared in future scholarly communication; i.e. it’s a kind of social experiment to see what are the digital artefacts that people wish to share and publish, to drop into the tooling of digital research. From this we’ve defined the notion of “Research Objects”, which are reusable, repurposeable, repeatable, reproducible, replayable, referenceable… lots of R-words, most recently including repair and release. Whichever of these we are doing, the key word might be reconstruct – the ability to reconstruct software apparatus, experiments and results. And Research Objects can be used by machines as well as people.That’s what we want, but what we have today is academic papers. The question is, what is the future of the paper so that we can reconstruct digital research? This is hotly debated and probably the printed and PDF copy are not the answer. One important innovation is the arrival of data journals and the new journals which treat software as a first-class citizen, like the Journal of Open Research Software, and Source Code for Biology and Medicine. Important steps along the way, but still a way to go.And so here’s an interesting opportunity for software experts. We have discussed how the assembly of software apparatus enters the research record so that we can reconstruct our apparatus. But assembling the digital artefacts of experiments share many aspects of software – digital, sometimes executable, volatile. The software community might have some very good ideas for the future of the experimental research record, beyond the data and software journals and for machines as well as human readers.Hence I believe the vibrant “sound software” community could lead the way in setting best practice with sustainable research objects, not just software. Already I know many researchers routinely adopt some software development tools to facilitate paper preparation. Github for MIR experiments anyone?

Slides

Special thanks to Kevin Page and Sean Bechhofer for their reflections on Research Objects and MIR, to Stephen Downie for running the sociotechnical infrastructure that is MIREX, and to Ichiro Fujinaga for the third corner of the SALAMI triangle (sociomusical?)

Many posters are made just before conference due to procastination the desire to show the latest results. How can you recognize such posters?Tweet

As it is still British Homeopathy Awareness Week, and as I genuinely do want to become more wary aware, I’ve conducted a little more web-searching to see what is going on in terms of wariness awareness-raising. Aside from the fallacious resort to celebrity name-dropping (also picked up on elsewhere), I still cannot find much underway in Britain. Which ought to please – although I’m sure plenty of them are likely up to their soothing ways. Wonder how much arnica they’re shifting.However, searching also brings up links to last April’s World HAW, the theme of which – infertility – I found perplexing and somewhat disturbing. And, continuing back down that path, my search brought forth this company ‘Natural Remedies’, offering a whole range of stuff, including under the sub-heading ‘Conception’:bq. ‘Homeopathic fertility treatment for healthy conception and free advice on conceiving’Two products feature here, named: Conception Flower Essence and Bringforth Life Flower Essence. If I click on the link for details of the former, its dedicated page is headed:bq. ‘Homeopathic remedies and flower essences for conception’We’re informed that this product, now fully named Conception Flower and Gem Essence, ‘Prepares the Mind and Body for New Life’. Hmmm. Reads like wonderful stuff. As I’m thinking, ’What’s in it?’ they’ve read my mind. Scrolling down under ’ What is NaturalEco Conception Essence?’, I see that:bq. ’ Conception Essence is a unique combination of flower and gem essences in pure, undiluted stock strength.’ (My emphasis in bold.)You spot the paradox? Homeopathic? Undiluted? Could it be that I’ve been misunderstanding something about homeopathy all along? Well, being genuinely confused, I decided to make use of the site’s ‘ask us’ page, and rattled off the following:bq. ‘Dear Sir/Madam,bq. I am interested in acquiring further information for your ’Conception Flower Essence’ and ‘Bringforth Life Flower Essence’ products.bq. I am unclear as to whether either or both of these is a homeopathic product. If so, could you comment on their potency: ie on the C dilution of their respective ingredients?bq. Thank you.‘Which I think is fair enough. Actually, the Bringforth Life Flower Essence dedicated page is headed:bq. _’Herbal remedies for infertility and flower and gem essences for healthy conception’_and as this one is also filed under ’ – Conception Difficult’, as distinct from ’ – Conception Typical’, it could be that it does possess some oomph in actually having stuff in it, whereas the ‘Typical’ product doesn’t need any, relying merely on homeopathic ‘memory’ of listed ingredients. (If so, I wonder whether it thus comes with instructions to succuss before use.) But this would seemingly contradict ‘undiluted stock strength.’ In my technical ignorance experience, I do not always get replies to messages sent via website e-mail facilities. So, having not received a response, I don’t know whether my message got there or not. As such, the stipulated 48 hours response time having elapsed, I can but only take the website at its words. So, let’s have a look at some of those words…I’ll just focus on the Conception Flower and Gem Essence, as that is the one less ambiguously listed under ‘homeopathic’. Whatever, it sure reads like a powerful cocktail. And after all, plenty of plant products do have very tangible effects, including alleviation of stress and anxiety (or so I gather, for some people). And stress and anxiety may well interfere with the body’s procreative functions from time to time. But can the ingredients listed here alleviate such problems? The marketing language at work assures us so.For example, we learn that Pomegranate ‘contains harmonizing qualities which bring clarity of thought and emotion’. Wild Iris opens ‘the creative channels… freeing the individual of self-doubt and wariness of their creative potential.’ (Wariness? Hey – perhaps this is what I need.) Think what could be achieved; plus it reads as though life is rendered one long party: it ‘raises the feelings of joyful anticipation and deep connection with the universe.’ Wow – a fella could have a pretty good weekend in Amsterdam with a crate of this stuff!But Flowering Cherry Essence makes me (even more, if that’s possible) incredulous: it ‘brings out the gentle nature of the soul.’ Ahh, you see, it won’t do you any good unless you believe you have a soul. This is not the only example of religious-lite language here. Not dissimilarly, Pink Camellia Essence ‘nurtures the mothering spirit within all women… Helping to heal the spirit of the lost mother within.’Nevermind the contra-homeopathy polypharmacy here. I’m afraid I then become further confused. The final three ingredients on the list are ‘gem essences’. Uh? You can get ‘essence’ from a gem? A stone!? Nevermind imagining some grinding and extraction process that purifies and concentrates a stone’s supposed characteristic nature in material form (which I think I prefer to consider over some emanating ‘field’ – an ethereal essence – which can be captured by immersing stones or crystals in the liquid during preparation). Just take their word for it that Aquamarine is ‘helpful in steadying and clearing the spirit’; that Citrine ‘integrates the physical and spiritual’ (regardless of whether it carries the rays of the sun or not); that Tourmaline ‘helps to release and dispel negative and painful emotions.’ Fascinating stuff.Well, I am not an authority on any supposed healing properties of these flowers, nor of any capturable essences that solid gemstones might possess. For all I know there may be copious scientific literature, the citing of which the site’s authors confidently consider superfluous and/or irrelevant. A lot of people believe this kind of stuff, so… (… err… I’m not sure how to finish this sentence). I guess it might smell nice (although that would suggest it is not homeopathic), which is handy because, as it can be applied undiluted to external areas, it can double up as perfume. Smelling more rat-like, however, is the statement:bq. ‘Conception Essence, like all our Flower and Gem Essences, is a vibrational healing medium and can therefore be introduced to the aura energy field in a variety of ways.’‘Aura energy field’? Yep, we’re into crystal/Reiki/chakra/homeopathy wacko territory alright. ‘Vibrational’? What, on account of the piezoelectric effect as possessed by one or two of those gems? Surely the real vibration of a spin-cycle washing machine would be more conducive to conception. So what ‘evidence’ is provided? Well, will a few satisfied customer Testimonials suffice? (I am always suspicious when this device appears in any promotional material, regardless. Where are the dis-satisfied ones?) Again, let’s take it that these are real unsolicited statements by real people. So, has no one thought it worth pointing out to ‘Nikki V.’ that, for all she knows, her pregnancy would have been trouble-free anyway, irrespective of her sister’s experience? Or would that be spoiling the fun? Read the others, if you need convincing.If you think this all annoyingly patronising, just continue on to read ‘What else is important at this time?’ Although the site is seemingly pitched at consumers bereft of common sense, one might reasonably presume that the company believes in its products; and the flowery emotive language it uses to promote them. Yet reading the lengthy disclaimer at the bottom of the pages, I’m not too sure. And I’m still unclear, despite the overlap in some of the fuzzy pseudoscientific terminology (‘natural’, ‘energy’, ‘healing’, ‘vibrational’, etc), as to whether Conception Flower and Gem Essence is a homeopathic product or not. I’ll let you know whether they get back to me on that one. Enjoy the rest of the ‘week.’

(Edison’s notebook)
“The successful scientist thinks like a poet but works like a bookkeeper.” E. O. Wilson

Writing in one’s lab journal is not frequently seen on lists of ‘top reasons why I became a scientist’. As an undergraduate student I hated lab journals with a passion. It was no fun writing things down when I wanted to proceed with the actual experiment, and it was even less fun trying to decipher my hastily-scribbled notes six months later while working on the report. Based on bitter experience, I started to grudgingly accept lab journals as a necessary evil of scientific life – until, not too long ago, my investigations into the lives of the great scientists hinted I may have grossly maligned the poor lab journal. Most great scientists had lab journals and/or produced voluminous quantities of writing, and there are even some indications that labjournalling in the right way may not have been a bitter duty to them, but a valuable resource in becoming even more brilliant. Sounds strange? Let’s look at the findings.

One of the first scholars of genius was Lewis Terman at the start of the 20th century; he and his student Catherine Cox compiled huge lists of geniuses, including estimated IQs, personality descriptions and biographies. One of their conclusions was (if one is to believe the reference to their work by Michael Gelb’s “Discover your genius”) that geniuses ‘wrote a lot’. Newton, Huijgens, Edison, Faraday, Lord Kelvin all wrote fanatically in their laboratory notebooks, Einstein and especially Darwin wrote many, many letters to friends and colleagues (Darwin alone over 15,000 letters). Interestingly, this also held for geniuses in ‘less scientific’ domains, such as composers (Mozart) and painters (Van Gogh), who also produced quite striking quantities of letters. Did those geniuses write so much because they were geniuses, or were they geniuses because they wrote so much?

In case of the great scientists, if writing indeed helped them become geniuses, the act of writing could not have been the only factor. After all, most journalists and novelists write all day long, but they are seldom regarded as geniuses. But there are differences between ‘genius’ writing and ‘professional’ writing. First of all, genius scientists may actually write many more words than professional journalists; after all, a journalist can take a few hours to write a few hundred words, since the article, to be a success, must be readable and interesting for a lay audience. Journalists and novelists are not so much writers as they are re-writers and editors. A scientist generally does not need to be concerned about style when writing in a lab journal, or writing letters to friends. Secondly, journalists tend to write over a wide range of subjects, thereby lacking the specialisation necessary to develop thorough expertise in a single area. Finally, journalists probably often write about matters in which they are not very interested personally; thereby probably learning less from texts than great scientists and geniuses in other fields.

But do we actually have more evidence for ‘genius-boosting’ writing than Catherine Cox’s research? One additional hint comes from psychology; cognitive psychology for example can treat a significant proportion of depressed patients quite well by requiring them to write their thoughts down – and other scientists have even found that writing about your problems is much more effective in helping solve them than talking about them (as reported by Richard Wiseman in his book ‘59 seconds’) At the moment, we are not certain why this is so; it could be that writing prevents thoughts from running aimlessly in circles. Alternatively, writing things down frees working memory which can then be used for ‘thinking about thinking’ (metacognition); for example, ‘maths wonders’ who can do sums extremely quickly in their heads actually calculate faster if they are allowed to use paper; the ‘external memory’ of paper frees working memory so they can use more efficient algorithms. A third possible mechanism is that writing things down can function as a so-called ‘elabotive rehearsal’, which sinks facts more solidly in memory than mere ‘internal’ repetition could.

The biographies of scientists are another source of hints that there may be something useful in ‘writing well’; Irving Langmuir’s parents, for example, exhorted him to observe nature carefully and make detailed notes. John Dalton, the inventor of atomic theory, kept elaborate and accurate records of the weather; there does seem to be something about writing things down, especially if you strive to record (and observe) accurately.

The final hint that writing mayt work is that testing the theory seems to confirm it. For example, for a period I wrote half an hour a day based on a statement in the book ‘how to get everything done and still have time to play’ (Mark Forster) that writing about both your observations and your feelings about them would increase your intelligence. And truly, I did feel smarter for the first week or two. In my case, however, the effect seemed to fade after a few weeks since I began to focus more and more on the writing cramp in my hand instead of on the challenges in my life. Still, if I had known as much about great scientists and talent development as I know now, I would probably have focused on stopping the writing when I would lose interest or develop distracting cramp, and either pause or try find a more intereesting subject to write about.

In conclusion, writing in a certain way seems to help your scientific prowess. At the moment, I’d guess the ground rules would be something like:


1) write about what you find important/interesting

2) write/observe accurately

3) don’t bother about making things readable/attractive for everyone; lab journal writing serves to give you alternative ideas about a problem, strengthen your memory and free space from your working memory.

4) feel free to write about your feelings, your dreams, even little poems if you feel like it; if something is in your mind, write it down so you can get on with other business without it needlessly cluttering your brain.

5) when you feel bored, or for whatever not able to concentrate on the writing, stop and go do something else for a while.


So, if you today are a young scientist, or even an older scientist, it may definitely be interesting to experiment for a month or so with writing lab journals and letters in a ‘genius-like’ way; there is definitely more to find out about it, but based on the data we have now, keeping a good lab journal or other notes does seem valuable to a scientist trying to get as great ideas and do as great research as possible. Lab journals may never feature on the lists of “top ten reasons why I became a scientist”, but who knows: it may very well be that, in the end, you will list your humbe journal on another list, the list of “top 10 reasons why I became a really great scientist”.