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Geologic methane seeping from thawing cryosphere (from Liz O'Connell's blog)

Tue, 06/26/2012 - 7:55pm

Cryosphere_Methane.jpgMethane-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.

Small Scales, Big Ideas - Nanodermatology at the Society for Investigative Dermatology (from Lowell Goldsmith's blog)

Tue, 06/26/2012 - 10:00am

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 HillNanodermatology.jpgThe 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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Today's quiz: explain the obscure site (from Bob O'Hara's blog)

Tue, 06/26/2012 - 8:16am

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.

A little Natural History with Hitchcock (from Mike Fowler's blog)

Mon, 06/25/2012 - 6:04am

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.IMG_0040.JPGAre 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,IMG_0041.JPGWell 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.IMG_0063.JPGGo 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.IMG_0065.JPGI 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?

The Gatekeepers of Sunlight (from Paige Brown's blog)

Sun, 06/24/2012 - 1:23am

NASA ISS024-E-15122.jpgManaging 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.bq. 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.IMG_8741.JPG 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: Vaccine Factories For HIV (from Nsikan Akpan's blog)

Sat, 06/23/2012 - 10:03am

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.  

Fig1 Subtypes.jpg     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.


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

Science: girl things make you wince (from Bob O'Hara's blog)

Fri, 06/22/2012 - 9:56am

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:

Sound Scholarly Communication (from David De Roure's blog)

Thu, 06/21/2012 - 5:13pm

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?)

Last minute posters (cartoon) (from Viktor Poor's blog)

Wed, 06/20/2012 - 9:08am

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

Still... Homeopathy Wariness Week (from Lee Turnpenny's blog)

Wed, 06/20/2012 - 7:56am

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.’

Genius writing - or can a good lab journal help you become smarter? (from Eric-Wubbo Lameijer's blog)

Tue, 06/19/2012 - 5:40pm

EdisonNotebook.jpg(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”.

Flying machines for the dirty, dull and dangerous (from Liz O'Connell's blog)

Tue, 06/19/2012 - 4:34pm

by Ned RozellSome places in this world are just too dirty, dull or dangerous for human pilots to fly. An airspace in the latter category is anywhere near gas flares in Alask’s oil fields.With only a few seconds of warning, flames blast high in the air from a network of pipes, releasing the stress of sucking oil from deep in the ground.Greg Walker recently found himself taking a look these fire-breathing nozzles near Prudhoe Bay, but he was barely close enough to see them from where he stood. He instead watched a “flying king crab” that buzzed around flaming flare heads 50 feet above the ground.UAV aircraft Aeryon ScoutAn Aeryon Scout flies over the shoreline of Prince William Sound near Valdez during an exercise in summer 2011 to check its usefulness in oil spill cleanup assessment.The 2.5-pound flying machine captured video and five-megapixel images of the flares and their support pipes, some of them jacked by frost and needing repair.Walker’s mission was to help oil-company workers for BP order expensive parts they need to replace during scheduled maintenance next summer. He used one of BP’s Aeryon Scouts, a four-propeller flying machine BP had purchased for use on the Deepwater Horizon oil spill.BP collaborated with Walker and his team because they are experts on operating unmanned aerial vehicles.As the manager of Poker Flat Research Range, part of University of Alaska Fairbanks’ Geophysical Institute, Walker is assembling a fleet of these tools in an enterprise that makes he and his team very busy.After visiting Prudhoe Bay to inspect BP’s flares, Walker was off to Kodiak to fly the Scout over the shoreline. He wants to use the flyers to see how harbor seals react to launches from a rocket facility on Kodiak Island.This is after a summer in which he and his crew traveled to Prince William Sound to test the Scout’s ability to buzz over beaches to help crews plan oil spill cleanups and out to Dutch Harbor to see how effective a larger, fixed-wing flying machine was for mapping gatherings of Steller sea lions.The unmanned aerial vehicle business is on the rise in Alaska, as more agencies come to UAF to work with Walker and his crew at Poker Flat.The university now owns nine Scan Eagles — 40-pound aircraft the size of California condors that the crew has used to map the boundaries of smoky wildfires and to count seals in the Bering Sea — two of the lunar-lander type Scouts, two similar models with more propellers than the Scouts, and three smaller aircraft launched by catapult.Two summers ago, Walker and Don Hampton spent a month aboard a ship with biologists who were looking for seals that live on and around the northern ice.Walker and Hampton flew missions with a camera they installed in the aircraft’s nose.The camera captured more than 25,000 images, often on days that featured crummy weather, which underscored the Alaska niche for unmanned aerial vehicles.“It’s hazardous to put humans out there,” Walker said. “If you’re out there (in a small airplane or helicopter) hundreds of miles from land, 400 feet altitude, if you have any problems at all, you’re dead.”Walker, who ran his own company that designed and made control systems for unmanned aircraft before coming to Alaska in 1998, said the opportunities keep coming for his team, which includes Hampton, David Giessel, Kathe Rich, Ro Bailey and Jeff Rothman.During the next couple of years they will use unmanned flying machines to help sea-ice researchers, to sample volcanic ash and to monitor endangered Steller sea lions in the western Aleutians.“The more you show the capability of these things, the more people come up with needs for them,” Walker said.Find more on Alaska’s Unmanned Aircraft Research at Frontier ScientistsOriginally published in the Alaska Science Forum November 29, 2011 Flying machines for the dirty, dull and dangerous by Ned Rozell http://www.gi.alaska.edu/node/941"This column is provided as a public service by the Geophysical Institute, University of Alaska Fairbanks, in cooperation with the UAF research community. Ned Rozell is a science writer at the institute."

Inspirational Daze (from Lowell Goldsmith's blog)

Tue, 06/19/2012 - 12:00pm

Flickr-photograph-by-Sören 'chucker' Kuklau.jpgKaleidoscopic vision is the best way to experience the 2012 annual meeting of the Society for Investigative Dermatology (SID). The meeting celebrated the 75th anniversary of the SID, and the spirits of its founders filled the Raleigh, NC convention center. Many of their pictures were on medallion decals in the entrance hall. These decals celebrated the past, and modern QR codes connected the medallions to articles about these individuals and their times.Another inspirational exhibit was the reproduction of Stephen Rothman‘s notebook documenting his displacement from Hungary and his relocation to the University of Chicago, where he performed and recorded pharmacological studies on his own skin. The oral and poster presentations, many by dermatology residents and fellows from around the world, inspired attendees with new data related to skin biology and skin diseases. The role of new technologies related to genomic sciences was impressive — everything from immunological mechanisms, to tracing hospital epidemics of serious infectious diseases, to determining the etiology of very rare congenital and genetic conditions that had resisted routine genetic testing were discussed. High school students from the North Carolina School of Science and Mathematics in Durham, NC added to the youthful energy, and the students used the historical medallions on the floor for hopscotch, reminding us that the young think out of the box – and reminding us of the joy of play.Five days later at the near-by concert Hall, Itzhak Perlman played the Tchaikovsky Violin Concerto in D Major with the North Carolina Symphony Orchestra: another kind of inspirational performance, where the performer and audience were rapturously engaged with a challenging concerto. Using a 300 year old Stradivarius, Perlman captivated the audience, demonstrating that (admittedly, depending on the task) technology need not always be the newest. The performance took the complete commitment of a diligent master performer completely integrated with his supporting orchestra — not very different from the lecturers at the SID, whose orchestras of supporting junior and senior scientists allow their ideas to soar. May all performers of science and the arts practice hard and play on for their committed audiences, who turn to them for inspiration.(the image is from Flickr and attributed to Sören ’chucker’ Kuklau)TO COMMENT:Be sure you are signed in to your Nature.com account.(You can sign in using the link at the upper-right of the page; it’s a little hard to see – light blue against the black bar at the top of the page.)Once you are signed in, SCROLL to the bottom of the post, and enter your comment in the box provided. (Be sure to click “submit”.)No box? Click the “Permalink” link, then scroll down again.We look forward to your comments!

Geek Hop (from Mike Fowler's blog)

Tue, 06/19/2012 - 6:54am

It’s been quiet around here recently. I’ll update on forwhy before too long, hopefully. But for now, I’ll briefly say that changes are afoot.In the meantime, enjoy some of what I can only assume will surely be the future of the music industry.As I like to call it, Geek hop. And that’s a good thing.For more information on the excellent artist, Gripp, aka Marshall Gillson (he’s even got a geek name), start here: Skeptics’ Guide to the Universe

The Only Way Is Ethics: The Skeptical Economist reviewed (from Tom Webb's blog)

Tue, 06/19/2012 - 6:15am

I do not object to value judgements and political beliefs creeping into economic argument: I think they are inevitable. But then I do not claim economics as a science.Much of the furore that greeted the publication of Bjorn Lomborg’s The Skeptical Environmentalist back in 2001 focused on Lomborg’s credentials (or lack of them) to write it. Here was a statistician (and furthermore, one with effectively no academic track record) blithely using questionable statistics to claim that legions of environmental scientists had been getting it badly wrong for years.I have no such concerns over Jonathan Aldred, author of The Skeptical Economist (Earthscan, 2009)1. Aldred is a Lecturer in the Department of Land Economy and Fellow of Emmanuel College, Cambridge, and has trained in (and taught) the subject he dissects so well in this book.No, I worry instead about my qualifications as a reader: Am I perhaps too credible? I know that I am favourably inclined towards critiques of mainstream economics, particularly as implemented in public policy; I’m broadly sceptical of the ‘growth above all else’ agenda; and I lack the basic training in economics to separate balanced argument from polemic. But Aldred’s focus on evidence and data (concepts I do understand pretty well), and his careful analysis of numerous case studies, give me some confidence that his central thesis – essentially, that you cannot separate economics from ethics – is worthy of very careful consideration2.The economy dominates contemporary political discourse. Different political tribes might argue either for austerity and deficit reduction or for tax and spend, but all of them have one end in mind: economic growth3. This is such a central tenet of economic orthodoxy that it is never questioned in the practice or reporting of mainstream politics. John Humphries has never, to my knowledge, growled ‘why is growth good?’ to a cowering junior minister. Likewise, ‘economic growth’ has been allowed to become enshrined as a primary goal of all UK research councils4 with not a whimper of dissent. Contrast this with the outcry when the Arts and Humanities Research Council referenced the ‘big society’ in its strategic plan last year – dozens of senior academics threatened to resign over what they thought was an overt political agenda being forced upon them. But as Aldred makes abundantly clear throughout his superb book, the pursuit of economic growth is just as political as the ‘big society’ – it’s just not party political. Yet this orthodoxy “…leaves something crucial out. Economic growth is not an end in itself. We should focus instead on our quality of life, our well-being, or to rehabilitate an embarassing word, our happiness”.Much of the rest of the book is a dissection of economic orthodoxy as applied in different contexts. Although Aldred is careful to differentiate between the academic study of economics and its application in public life by what he terms ‘policy entrepreneurs’ – well, suffice to say that my opinion of mainstream academic economics was not significantly enhanced (with the old ’that’s all very well in practice, but how does it work in theory?’ caricature still to the fore). If you’re into this kind of stuff, some of the content may be familiar (e.g. the breakdown of the relationship between income and self-reported happiness above a – surprisingly low – threshold is in Clive Hamilton’s Growth Fetish; the negative consequences of introducing markets where they don’t belong is the subject of Michael Sandel’s What Money Can’t Buy) but it is covered here in more depth than I’ve read before, including why this might be the case (for instance, we adapt very quickly to increasing income, and then want still more). There is also a fascinating chapter dedicated to happiness actually means, whether self-reported or ‘objectively’ measured (and if, indeed, any such measurement is even conceptually possible).Other ideas were completely new to me. If you haven’t heard of Baumol’s cost disease (I hadn’t), it appears to be very important. Simply put, services like healthcare and education will inevitably become more expensive relative to other sectors of the economy, because one of the things we value most in them is their inefficiencies (in economic terms): lots of personal contact with a doctor, small class sizes, and so on. The important thing is that this is the case regardless of whether the service is provided by the state or by a private company. Privatising the NHS won’t make it more ‘efficient’, in other words (or at least, not relative to gains in efficiency elsewhere in the economy).Aldred also suggests some alternative goals for public policy. For example, instead of a constantly growing economy, why not keep it stable but allow all of us to work progressively less? (Sound crazy? Perhaps, but it’s a popular idea in France, and among the first significant acts of the new Socialist President Hollande was to reduce the retirement age for some workers to 60.) But the chapter most relevant to my professional interests is that on ‘Pricing Life and Nature’.Of course, this is a hot topic in ecology and conservation right now. Not just in Rio+20: think also of the Milennium Ecosystem Assessment, or big new UK initiatives on Valuing Nature, Biodiversity & Ecosystem Services, Ecosystem Services for Poverty Alleviation… Everyone wants to know, what can nature can do for us? Nobody disputes that the answer is ‘lots’ (from climate regulation to pollination to food provision) but going a step further, and putting a value on these services, is much more controversial – not least for many because it suggests that there is a cost-benefit equation somewhere which could, potentially, be balanced a different way. Suppose we could replace pollinating insects with cheap, effective and safe nanobots. Could we then do away with bees with a clean conscience?The counter to this unease, which I’ve heard expressed at VNN meetings, is to argue that the alternative to putting a value on nature is that its value will be assumed to be £0 in any planning and development decisions. But in that case, what we should be doing as scientists? Should we buy into this system, and spend our time trying to make our dubious numbers somewhat less dubious, supplying more and more refined nutriment to the cost-benefit beast? Maybe, but as Alred notes, unfortunately “dubious numbers are infectious: adding a dubious number to a reliable one yields an equally dubious number”. So we have a lot of work to do if we take that approach, and the numbers we produce may always be too dubious to be useful. Alternatively (and this seems to be Aldred’s preference), we could build better ways of incorporating qualitative pros and cons more transparently into the (overtly political) decision-making process.One of the real strengths of this book is Aldred’s ability to lay out options and consequences without preaching – this is certainly not a zero-growth, Occupy movement manifesto. Rather, it’s a sober analysis of the evidence (or lack of it) behind various policy decisions, and above all a call for us to recognise the politics that are integral to all decisions made (even those dressed up as ‘objective’ following cost-benefit anlayses). This is important stuff, and Aldred has done us all a service by producing an approachable primer on a topic which affects all of us, and the environment we depend upon. 1One assumes that the retention by Aldred, a British author, of the American ‘k’ is a subtle dig at Lomborg’s faith in mainstream economics.2Of course, the ongoing collapse of the world’s financial systems provide a pretty strong supporting case…3Or more specifically, growth in GDP, which seems even more ridiculous in the light of the double figure drop in GDP the UK would suffer if we all paid off our credit cards tomorrow – GDP depends on us spending money we don’t have! (I heard this discussed as if it was perfectly natural and sensible on a serious Radio 4 economics programme, but was listening in the car and don’t recall specific details.)4e.g. From the RCUK homepage: “We support excellent research, as judged by peer review, that has an impact on the growth, prosperity and wellbeing of the UK”

...what I used to think about science & research in Memes (from Linda Lin's blog)

Sat, 06/16/2012 - 8:00pm

What I thought about science during undergrad…What my friends think about science and what I thought about scientific research before grad school…and how i think I look B-)What I actually did during grad school… Get psyched about experiments and new projects :DAdded 1 kb ladder into PCR products instead of loading buffer.Ran gel in the wrong direction. Forgot to add Taq.Transformed a vector into mutants with the same antibiotic resistance. All transformants can grow on selection media :/Spilled EtOH on 100 labeled eppy tubes with RNA/DNA samples for genotyping/RT-PCR. No labels on samples after a day or 3 days of extraction.Lab subjects get a virus and die or skew results.have not seen significant other in months. etc. etc. Have to write a new project proposal…..What happened while I was writing my thesis… What I thought about thesis writing during writing.

Homeopathy Wariness Week (from Lee Turnpenny's blog)

Thu, 06/14/2012 - 6:50am

British Homeopathy Awareness Week commences today, until the 21st. But, it seems to me, there is little in the way of awareness raising going on. Certainly not on the British Homeopathic Association site, which (in contrast to the WHA’s shameless promotion of World Homeopathy Awareness Week back in April) appears not to be too occupied with it:bq. ‘Every year between 14-21 June we encourage people to raise awareness about homeopathy.’but I can’t see a whole lot of encouragement going on thereawarenessweek.html.The Society of Homeopaths is a bit more excited, however, with some bleating on about sports injuries and arnica, a ‘remedy’ (homeopathic medicines are remedies) I gather is popular in the cult. And, along with a few of the stock trite reminders of how great homeopathy is, a few famous sporting names are dropped, thus resorting to that doubly logical fallacy: not appeal to authority; but appeal to celebrity as authority. These names, including the promiscuous ‘David Beckham’, were apparently cited as ‘evidence’ for homeopathy during the Homeopathy Evidence Check conducted by the House of Commons Science and Technology Committee a couple of years back.More up for it too is Heal Through Homeopathy, which also informs that the week exploits this year’s Olympics, with promotion of the claimed homeopathic benefits to the treatment of sporting injuries. So, cue some more shameless celebrity name-dropping, led with an arnica endorsing quote from one Linford Christie. bq. ‘I am a fan of arnica and recommend all the Athletes in my Street Athletics programme have it in their kit bag to help with sprains and strains.’Yeah, cheers, Linford. Arnica also seems to help Jayne Torvill. Well, it seemed to help her in 2009.Another site scrapes the barrel even harder, appealing to a Mail Online article by Sarah Stacey, who informs that she, along with her animals, has long benefited from homeopathy. She follows this by spinning a testimonial anecdote, and then deals her trump card… Gaby Roslin. Way to go, Sarah. I wasn’t aware that Gaby still fits the definition of celebrity. She doesn’t seem to pop up on TV a whole lot anymore (thank goodness). Nevertheless, she’s obviously still considered of sufficient celebrity kudos, such that The Society of Homeopaths is also happy to include her among this stellar list, which tops its promotional bullet-pointed criteria.Plenty more of ‘em here and here, if you need convincing. I mean, how can all these celebrities be wrong? And the most expensive painting ever sold was a portrait of a homeopath. How much more evidence do we need?I don’t know whom I distrust more: those who cheaply, scrabblingly appeal to these celebrities; or the celebrities themselves for lending their names (if they have) to these marketing gimmicks. (Wonder how many of them have signed this.) Because that’s what it is: not evidence, marketing. When celebrity is invoked in endorsement of homeopathy, be doubly wary.

Reflections ~ Thesis writing mind melds (from Linda Lin's blog)

Wed, 06/13/2012 - 8:00pm

“Writers aren’t people exactly. Or, if they’re any good, they’re a whole lot of people trying so hard to be one person. It’s like actors, who try so pathetically not to look in mirrors. Who lean backward trying—only to see their faces in the reflecting chandeliers.”F. Scott Fitzgerald (Taken from the Last Tycoon)kevindooley photography memory memory models.jpgFlickr CC kevindooley, photography, memory, mental model I was thesis writing I got a lot of edits/corrections and feedback from my supervisor. Which is nothing out of the ordinary in the process. I was happy to make changes as well (God knows how terrible my first drafts were. Supervisor = God). But it was always rather difficult to break out of the writing molds I’d begin with, and it took more effort to ponder how to reshape structures and sentences than freely write them. After a while of back and forths with corrections & re-writing..I really began to observe how different my supervisor’s style was to mine. So much so that it started creating images in my head. i.e. I could hear him talking in his thick Aussie accent and envision him sitting in his office. Everyone has a different perception on things and different ways of expressing the same things. And it’s not a negative thing, to the contrary, it’s great. It’s as the cliche saying is, two heads are better than one. You end up observing more together at different angles. Like two simultaneously published articles by two very different labs on the same protein and trend. They come to different conclusions and theories, while both can be equally interesting and relevant, they’re oddly not the same. Just depends on how you look at it. Take a reading break!Golden Cage, by The Whitest Boy Alive.“Half of the people can be part right all of the timeSome of the people can be all right part of the timeBut all of the people can’t be all right all of the timeI think Abraham Lincoln said that”I’ll let you be in my dreams if I can be in yours"I said that."~ Bob Dylan

Back into view III (from Lee Turnpenny's blog)

Wed, 06/13/2012 - 10:10am

What is the difference between those two statements?bq. ‘Demonstrated ability to manage own workload proactively and to work to multiple deadlines’bq. ‘Good at managing own time and workload’Tautology, no? Would you expect both to crop up on the same job application form? Well, when university HR denizens generate these things, nothing surprises me anymore. But it still exasperates, nonetheless. (By the way, the subject of my previous rant along these lines did actually result in an interview. Which was very nice… but they didn’t appoint… anyone.)Never mind that the repetitively sectioned skills descriptions boxes do not tally with the Job Description and Person Specifications. Such that you are not exactly sure which position you are actually applying for. Moreover, all skills being now considered ‘Essential’; merely ‘Desirable’ no longer applies. Baffingly, this latest HR nugget, as well as requiring your CV details to be transposed into all the relevant boxes, also allows you to attach the bloody thing! But, when addressing the ‘statements’, you are informed that stating ‘See attached CV’ is not acceptable as an answer.I guess they want to assess how well you can write. On which, I suppose I am just going to have to accept playing this game. Because there aren’t that many jobs I want to do … being determined not to go back into the lab (which I don’t assume would take me anyhow). Problem is, then, what is there? Having entered the words ‘science’ and ‘writing’ into job search specifications upon registering with agencies and databases and job websites, every day I find my Inbox polluted with lots of this kind of thing:bq. Sales Rep, Sales Manager, Healthcare Advertising Agency, Healthcare PR Company, Healthcare Branding, Healthcare Advertising and Branding, Contracts Specialist, Consumables Sales Rep, Account Director, Client Services Director, Instrument Sales Rep, Bioproduction Sales Rep, Key Accounts Manager, Market Research, Liaison Executive, Sales and Marketing, Sales (Support) Specialist, Pharmaceutical Sales Specialist, Laboratory Business Manager, Account Director, Marketing Manager, Medical Educations and PR Agency… and so on and so forth, ad infinitum, ad nauseam_._Exhales long discontented “Sighhhhhh”.Oh, didn’t get an interview for the tautological position.If this continues, I might have to scratch that peripatetic itchiness. Except I can ill afford it.

Unmanned Aircraft: Arctic Science & Tech. (from Liz O'Connell's blog)

Tue, 06/12/2012 - 8:53pm

Aircraft_NOAA-UASlaunch.jpgNOAA: Launching an Unmanned Aerial Vehicle (UAV)Laura Nielsen for Frontier ScientistsSpeeding over Arctic sea ice, small remote-controlled aircraft snag video footage and high-definition shots of endangered Steller Sea Lions in their natural habitat. Quiet and unobtrusive, the machines can serve as Special Op.s for researchers. Low-altitude remote sensing using Unmanned Aerial Vehicles (UAVs) has vast potential… and we’re only beginning to explore it. Gregory Walker, the manager of the unmanned aircraft applications program at the University of Alaska Fairbanks Geophysical Institute, has been putting UAVs to good use, exploring their potential on the Alaskan Frontier. “The more you show the capability of these things, the more people come up with needs for them,” Walker said. He tests UAVs at the Poker Flat Research Range outside of Fairbanks, in addition to flights in the field.Aircraft_SEALIONS-NOAA-TaylorNobles.jpgNOAA: Taylor Nobles: Sea Lion hauloutUAVs perform well: surveying marine wildlife, in climate change studies, for pathfinding missions and as aides in emergency response plans, and accessing remote, hard-to-see or dangerous areas like active wildfires, volcano sites or oil spill areas. In January 2012, the Russian tanker Renda moved to deliver more than 1.3 million gallons of gasoline to Nome, Alaska. The Coast Guard Cutter Healy ground a path for both ships through sea ice toward Nome. As the ships approached, a team from the University of Alaska Fairbanks used UAVs to shoot images of the ice cover and engage in ice profiling. Those pictures let personnel gauge ice thickness and plot the safest route toward Nome. (It was yet one more way in which many technologies came together during the voyage to Nome.) UAVs have proven themselves capable of operating in inclement weather, low visibility, and weather with icing potential.Aircraft_NOAA-McArthurII.jpgNOAA: the McArthur II (from an earlier UAV launch test)In the Arctic, where the possibility of oil spills is increasing with increased offshore oil development, UAVs have promising applications for oil companies. Besides being used to conduct wildlife surveys in threatened areas, they might examine shorelines if a spill occurs. While assessing the Deepwater Horizon oil spill, British Petroleum used propeller-driven flying machines called Aeryon Scouts. For prevention instead of cleanup, UAVs can also serve as inspectors. In November 2011, Gregory Walker flew an Aeryon Scout at a BP oilfield near Prudhoe Bay. There, 50-feet tall machinery and pipes release flames to the atmosphere to relieve pressure in oil wells. The images Walker captured let workers determine what pipes needed repair or replacement, without putting any humans in danger.Similarly, the flying machines can fly in response to natural disasters. They can sample volcanic ash right out of the air over uneasy volcanoes, where fumes and the risk of ash-clogged engines keep manned flights away. UAVs can engage in Aerosol Collection, taking air samples to assist in studying the atmosphere or particle pollution. Scan Eagles, UAVs roughly the size of a California condor, have been used to track the edges of forest fires in smoky conditions, safeguarding firefighters. Alaska has even utilized UAVs in disaster-response exercizes. Responding to a large earthquake, for example, will be easier when responders can swiftly analyze the extent of damage to communities via aerial view. And UAVs can be launched with less prep. work than manned aircraft. They don’t require a runway, cell-phone connection, or large ammounts of fuel, making them ideal in remote Arctic locations.Aircraft_SEALIONS-USFWS-RoyW.Lowe.jpgUSFWS: Roy W. Lowe: Steller Sea LionsResearchers launched their UAVs in March 2012 off a ship the size of a fishing vessel to research Steller Sea Lion communities. Where traditional flyovers would take pilots and biologists far out over the open waters of the Bering Sea into potentially harsh weather conditions, these test flights sent small UAVs to many seal gathering places in the western Aleutian Islands. The ability to take short flights during pockets of clear weather and keep personnel safe onboard the ship highlights the benefits of UAV use in the dangerous and unpredictable weather of the Arctic. The machines are even able to fly despite weather conditions that would ground manned aircraft. Besides the small copter-like Aeryon Scout, the team used an AreoVironment Puma AE, a small plane with a 10 foot wingspan that can fly for two hours. The two crafts used video, infrared, and photo to capture information from 54 different sea lion sites. Most were locations where sea lions return again and again in order to socialize and rest on land (or ice) called haulout sites. Barely audible at 70 feet, the very quiet UAVs were able to film the sea lions from closer altitudes than a plane without scaring them into the water (as large and loud manned planes generally do). The UAVs are operated via an electronic interface, and the pilot does not need to see them to fly them- he can rely on their camera feeds- making them extremely useful for wildlife surveying.Alaska is investing in the emerging field of Unmanned Aerial Vehicles, because they can serve many purposes in the Arctic and beyond. Gregory Walker notes that by understanding the potential and the limitations of current UAV technology we can find people the right tools to solve many of their problems. We look forward to more spectacular uses for these agile and impressive machines.Part of Frontier Scientists’ project: Unmanned Aerial Vehicles