November 8, 2009
Category: Medicine • SO'10 • Skepticism
You can listen to the Friday episode of Skeptically Speaking here. I am at the beginning, first 10 minutes or so, explaining what ScienceOnline2010 is all about. But the rest of the show with Paul Ingraham is very interesting as well.
Posted by Coturnix at 12:18 PM • 0 Comments • 0 TrackBacks
Category: SO'10
As you know, the Program is fully set now. There is a lot of stuff there! So, to help you out, I will post an occasional sample of sessions, organized by time - when they will occur during the conference.
So today, I'll start at the beginning, highlighting session that will happen on Saturday, January 16th, at 9:00-10:05am. Letters A-E denote rooms. You will notice that each session has its own page where you are welcome to post questions and commentary.
A. From Blog to Book: Using Blogs and Social Networks to Develop Your Professional Writing - Tom Levenson, Brian Switek and Rebecca Skloot
Description: Many bloggers have the desire to use their blogs as a springboard to larger writing projects, such as a book, but the details of this process are obscure to many aspiring science writers. In this session we will discuss the details of writing a proposal, finding an agent, using blogs as "writing laboratories", and making the most of the science blogging community in promoting your projects. Discuss here
B. Casting a wider net: Promoting gender and ethnic diversity in STEM - D.N.Lee and Anne Jefferson
Description: We will introduce programs that attract wider audiences to science, math, and engineering at various institutions/education levels, programs that mentor students (high school, undergrad & grad students) in research and education excellence. How Social Media tools can be used to raise the profile of and build support networks for under-represented scientists and engineers. Discuss here
C. Demos
- Science and the mobile device - Christopher Perrien
Description: A demo of iPhone Science Apps. Discuss here
- Trixie Tracker - Ben MacNeill
Description: Data-driven parenting - Trixie Tracker is a data tracking web and phone app that allows parents to tease out patterns in their children's sleep activity. Discuss here
- Text message based angler reporting method: twitter and fishcatch - Scott Baker
Description: In this demo, audience members will use their personal cell phones to text in fisheries effort and catch data to an online database that is updated in real-time. Participants will use wallet sized cheat sheets (included) and the simple syntax "rectext" to help them prepare fishing reports in the proper format. A brief overview of current fisheries projects as well as other potential applications will be discussed. Discuss here
- Google Wave for scientists - Cameron Neylon
Description: Google Wave for scientists who are complete n00bs Discuss here
D. The Importance of Meatspace: Science Motels, science freelancing and science coworking - Anthony Townsend and Paweł Szczęsny
Description: Science careers and science workplaces are undergoing dramatic change, driven by internal shifts in the practice of science and external shifts in labor markets and workplace design and management. This session will be split into two sections. The first half will explore the shift from freelance scientists to virtual contract research organization, and explore alternative models for R&D;. The second half will explore possible models for science motels and science coworking, building on the "research cloud" scenario presented in the Institute for the Future's "Future Knowledge Ecosystems" report, released in 2009 as part of the Research Triangle Park's 50th anniversary. We will use a group brainstorming process to develop a map of ideas about how freelancer scientists, virtual CROs and flexible lab/workspaces may co-evolve in over the coming decade. Discuss here
E. Podcasting in science - Deepak Singh and Kirsten 'Dr.Kiki' Sanford
Description: What role does podcasting play in science? In fact, it plays many. More than just a way to broadcast ideas, podcasting is the beginning of a conversation, it is the archiving of methodologies, it is news, it is marketing, and much more. We will discuss the many ways that podcasting technology and techniques can be used to help you reach your communication goals. Discuss here
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Category: Clock Quotes
That which we are, we are.
One equal temper of heroic hearts,
made weak by time and fate.
But strong in will,
to strive, to seek, to find, and not to yeild.
- Alfred, Lord Tennyson
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November 7, 2009
Category: SO'10
Ignite-style talks are very, very energetic. They last 5 minutes each and the slideshow is set to automatically change slides every 15 seconds. Thus, one cannot be slow or go over time. These kinds of talks can be very funny, yet also very powerful. At ScienceOnline2010, we will have an Ignite session on Saturday night, at the Radisson Hotel during the banquet/dinner. Here is the lineup of speakers and topics:
"Why Triangle is Better than Silicon Valley" - Wayne Sutton
"My "Little Black Book" of Scientists I Love" - Joanne Manaster
"Crowdsourced Chemistry - Why Online Chemistry Data Needs Your Help" - Antony Williams
"Blogging on the tenure track" - Janet Stemwedel
"Being mentored - not only for grad students" - Pawel Szczesny
"Dive Into Your Imagination" - Annie Crawley
"SARS, Drugs, and Biosensors" - Aaron Rowe
"The Story of NanoBioTechnology" - Mary Spiro
"Data mining the literature with Zotero" - Trevor Owens
"Games in Open Science Education" - Antony Williams and Jean-Claude Bradley
Posted by Coturnix at 10:28 AM • 0 Comments • 0 TrackBacks
Category: Clock Quotes
Keep on beginning and failing. Each time you fail, start all over again, and you will grow stronger until have accomplished a purpose - not the one you began with perhaps, but one you'll be glad to remember.
- Anne Sullivan
Posted by Coturnix at 4:00 AM • 0 Comments • 0 TrackBacks
November 6, 2009
Category: Tweetlinks
Follow me on Twitter to get these, and more, in something closer to Real Time (all my tweets are also imported into FriendFeed where they are much more easy to search and comment on, as well as into my Facebook wall where they are seen by quite a different set of people):
Scientwists Twitter List by David Bradley on Listorious
FLOTUS: Elevating the social status of nerds everywhere
An open letter to the medical community - Some passionate debate about personal genomics!
The Genomic Ark: 10,000 vertebrate genomes
Beautiful electron microscopic and computer modelling images from the new book by Frankel & Whitesides
Claiming to be unbiased is a patronising fairytale, so let's just own up to our agendas
International Wolf Center Podcasts
Knowledge as a public good
Get with the times, Jay Rosen tells journos
LOL - Republicans come up with their own Healthcare plan: Congressional Budget Office Thrashes Republican Health-Care Plan. Embarassing!
This is bad, this is very bad - shooting at Ft. Hood
Polarized News? The Media's Moderate Bias
For improving early literacy, reading comics is no child's play
The age of informavore
Deals and their consequences, reports on green technology & personalized medicine
Calculating Animal Intelligence and Top 10 Smartest Mammals
On the media (or press) - science journalism, right and wrong.
Reflections on Science 2.0 from a distance - Part II
Awesome computer animation (wmv download) by Animusic.
The Secret to Learning is Unlearning
Responsibility: Shane and Joe - Health Care Organizational Ethics: "For every lone cowboy, there's a community of support"
Response to Dan Ariely's Duke Sex Toy Study Is Predictably Irrational
World-Science podcast: Swine Flu in the Amazon, Fixing Technological Fixes, Tsavo Lions and forum: Making Technology Work -- for People with Anu Ramaswami.
Student journalists wage battle for H1N1 death certificates
Year of Energy 2009
Can We Talk About Science? I Mean, Really?
Pseudo-quackery in Pain Management: a field with a large gray zone between overt quackery and evidence-based care
How Would Los Angeles Look with No Cars?
Posted by Coturnix at 8:57 PM • 0 Comments • 0 TrackBacks
Category: Carnivals
Four Stone Hearth #79 is up on Anthropology.net
Friday Ark #268 is up on Modulator
Posted by Coturnix at 10:32 AM • 0 Comments • 0 TrackBacks
Category: SO'10
As you know you can see everyone who's registered for the conference, but I highlight 4-6 participants every day as this may be an easier way for you to digest the list. You can also look at the Program so see who is doing what.
Sol Lederman is the Consultant for US Dept of Energy Office of Scientific and Technical Information in Santa Fe, New Mexico, and a blogger. He also tweets for the Department. I interviewed Sol earlier this year, after his session at ScienceOnline'09. At the next conference, Sol will lead a workshop "Make your own social networking site with Drupal".
Chris Nicolini is the Web Producer and Editor for the American Institute of Physics and runs (and tweets for) InsideScience.org.
Lenore Ramm works at Duke Center for Instructional Technology, is an artist and a food blogger and a twitterer.
Tyler Dukes is a Web producer at News 14 Carolina and a freelance journalist in Raleigh, NC. He blogs on -30- and is on Twitter.
Ryan Somma is a software developer, works in USCG Aviation Logistics Center and is an amateur scientist at Port Discover Science Center in Elizabeth City on the coast of North Carolina. He blogs on Ideonexus and is also on Twitter.
Posted by Coturnix at 9:38 AM • 0 Comments • 0 TrackBacks
Category: Science News
Current Status of a Model System: The Gene Gp-9 and Its Association with Social Organization in Fire Ants:
The Gp-9 gene in fire ants represents an important model system for studying the evolution of social organization in insects as well as a rich source of information relevant to other major evolutionary topics. An important feature of this system is that polymorphism in social organization is completely associated with allelic variation at Gp-9, such that single-queen colonies (monogyne form) include only inhabitants bearing B-like alleles while multiple-queen colonies (polygyne form) additionally include inhabitants bearing b-like alleles. A recent study of this system by Leal and Ishida (2008) made two major claims, the validity and significance of which we examine here. After reviewing existing literature, analyzing the methods and results of Leal and Ishida (2008), and generating new data from one of their study sites, we conclude that their claim that polygyny can occur in Solenopsis invicta in the U.S.A. in the absence of expression of the b-like allele Gp-9b is unfounded. Moreover, we argue that available information on insect OBPs (the family of proteins to which GP-9 belongs), on the evolutionary/population genetics of Gp-9, and on pheromonal/behavioral control of fire ant colony queen number fails to support their view that GP-9 plays no role in the chemosensory-mediated communication that underpins regulation of social organization. Our analyses lead us to conclude that there are no new reasons to question the existing consensus view of the Gp-9 system outlined in Gotzek and Ross (2007).
Robust Models for Optic Flow Coding in Natural Scenes Inspired by Insect Biology:
Building artificial vision systems that work robustly in a variety of environments has been difficult, with systems often only performing well under restricted conditions. In contrast, animal vision operates effectively under extremely variable situations. Many attempts to emulate biological vision have met with limited success, often because multiple seemingly appropriate approximations to neural coding resulted in a compromised system. We have constructed a full model for motion processing in the insect visual pathway incorporating known or suspected elements in as much detail as possible. We have found that it is only once all elements are present that the system performs robustly, with reduction or removal of elements dramatically limiting performance. The implementation of this new algorithm could provide a very useful and robust velocity estimator for artificial navigation systems.
Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides:
Dehalococcoides are free-living sediment and subsurface bacteria with remarkably small, streamlined genomes and an unusual degree of niche specialization. These strictly anaerobic bacteria gain metabolic energy exclusively through a novel type of respiration that results in reductive elimination of chlorides from organochlorines, many of which are priority pollutants. In this article, we compare the first complete genome sequences of Dehalococcoides strains that grow via respiration of vinyl chloride (VC), a human carcinogen and abundant groundwater pollutant. Our work provides novel insights into Dehalococcoides chromosome organization and evolution, identifies specific positions in the chromosomes where new genes--like the genes responsible for growth on VC--are integrated, and generates clues how these dechlorinating bacteria adapt to anthropogenic contamination. This information sheds new light on Dehalococcoides biology and ecology, with implications for enhanced bioremediation to protect dwindling drinking water reservoirs.
Posted by Coturnix at 8:36 AM • 0 Comments • 0 TrackBacks
Category: Clock Quotes
I have often been downcast, but never in despair; I regard our hiding as a dangerous adventure, romantic and interesting at the same time. In my diary, I treat all the privations as amusing. I have made up my mind now to lead a different life from other girls.
- Anne Frank
Posted by Coturnix at 3:57 AM • 0 Comments • 0 TrackBacks
November 5, 2009
Category: OpenLab09
Here are the submissions for OpenLab 2009 to date. As we have surpassed 470 entries, all of them, as well as the "submit" buttons and codes and the bookmarklet, are under the fold. You can buy the 2006, 2007 and 2008 editions at Lulu.com. Please use the submission form to add more of your and other people's posts (remember that we are looking for original poems, art, cartoons and comics, as well as essays):
Read on »
Posted by Coturnix at 10:47 PM • 0 Comments • 0 TrackBacks
Category: SO'10
I'll be briefly on the Skeptically Speaking radio show tomorrow night at 8pm Eastern, introducing ScienceOnline2010. You can listen live here.
Posted by Coturnix at 10:00 PM • 0 Comments • 0 TrackBacks
Category: Blogging • Housekeeping
Having difficulties following the flood of blogging here on scienceblogs.com? Well, it just became much easier. Go to this page and find the widgets with all sorts of feeds: the Select feed, the Channels feeds and all the individual blog feeds. So, if you want my feed, you click on the Blogs (A-C) tab, find my blog, click on 'Share', click on the 'Install outside Netvibes' tab, then choose where you want to download it. Then pick the way you want it to look (there is a pull-down menu with several choices, as well as several colors to choose from), copy the widget code and paste it into your site (or iGoogle etc.) and you'll get something like this:
or something like this:
Then just click through if you want to read any individual post.
Posted by Coturnix at 6:36 PM • 4 Comments • 0 TrackBacks
Category: Carnivals
The 123rd Congregation of the Skeptics' Circle is up on Blue Genes - Science news
Posted by Coturnix at 6:33 PM • 0 Comments • 0 TrackBacks
Category: SO'10
As you know you can see everyone who's registered for the conference, but I highlight 4-6 participants every day as this may be an easier way for you to digest the list. You can also look at the Program so see who is doing what.
There are three parent-child pairs coming to the conference in January and all three have been here before:
John and Sam Dupuis are a father and son. John is the Head of the Steacie Science & Engineering Library at York University and a SciBling, blogging at Confessions of a Science Librarian. I interviewed John last year after the 2008 conference. His son Sam blogs on Science of Sorts on My Mind. He came to ScienceOnline09 with his Dad and I interviewed him as well. At the Conference, John will co-moderate the session on "Online Reference Managers". He can also be found on Twitter.
Tatjana Jovanovic-Grove and Djordje Jeremic are a mother and son pair, originally from my homeland of Serbia. They both came to ScienceOnline09 and are coming back for more. Tatjana is a biologist and an artist. Djordje is a blogger and an origami artist. I interviewed both Tanja and Djordje earlier this year. At the Conference, Tatjana will co-moderate a session on "Open Access and Science Career Hurdles in the Developing world".
Kim and Patty Gainer are the veterans of all four conferences. Kim teaches English and writing at Radford University in Virginia. She also writes fantasy fan fiction. Her daughter Patty is a student at New River Community College.
Posted by Coturnix at 9:58 AM • 0 Comments • 0 TrackBacks
Category: Earth • North Carolina • Science Education
Boom 'n' Doom: Volcanoes, North Carolina and North Carolina Volcanoes
November 18th; Acro Café on the fourth floor of the Museum of Natural Sciences
8:30-10:00 am with discussion beginning at 9:00 followed by Q&A
Volcanic activity half a world away can affect us in our own state. When Indonesia's Mount Tambora erupted over about 4 days in 1815, the resulting debris cloud led to the "Year Without Summer" in 1816, which was marked by massive crop failures from Europe to North Carolina. Join in a discussion of recent and historical world-wide volcanic events, and find out about old North Carolina volcanoes. Learn about the new Mineral Spectroscopy Laboratory and how Museum research is helping understand and ameliorate the effects of large scale volcanic eruptions.
About the Speaker: Dr. Chris Tacker has been the Research Curator in Geology for the Museum of Natural Sciences since 1996. His work involves mineralogy and its application to understanding geologic processes, especially those that involve fluids and big explosions. Recently, the National Science Foundation awarded him two grants for mineral spectroscopy. He also writes on North Carolina geology for the general public, and appears on the Museum's PBS program Exploring North Carolina.
RSVP: katey.ahmann@ncdenr.gov; or call 919-733-7450 ext.531
Posted by Coturnix at 9:17 AM • 1 Comments • 0 TrackBacks
Category: Science News
There are 22 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week - you go and look for your own favourites:
Improvements of Sound Localization Abilities by the Facial Ruff of the Barn Owl (Tyto alba) as Demonstrated by Virtual Ruff Removal:
When sound arrives at the eardrum it has already been filtered by the body, head, and outer ear. This process is mathematically described by the head-related transfer functions (HRTFs), which are characteristic for the spatial position of a sound source and for the individual ear. HRTFs in the barn owl (Tyto alba) are also shaped by the facial ruff, a specialization that alters interaural time differences (ITD), interaural intensity differences (ILD), and the frequency spectrum of the incoming sound to improve sound localization. Here we created novel stimuli to simulate the removal of the barn owl's ruff in a virtual acoustic environment, thus creating a situation similar to passive listening in other animals, and used these stimuli in behavioral tests. HRTFs were recorded from an owl before and after removal of the ruff feathers. Normal and ruff-removed conditions were created by filtering broadband noise with the HRTFs. Under normal virtual conditions, no differences in azimuthal head-turning behavior between individualized and non-individualized HRTFs were observed. The owls were able to respond differently to stimuli from the back than to stimuli from the front having the same ITD. By contrast, such a discrimination was not possible after the virtual removal of the ruff. Elevational head-turn angles were (slightly) smaller with non-individualized than with individualized HRTFs. The removal of the ruff resulted in a large decrease in elevational head-turning amplitudes. The facial ruff a) improves azimuthal sound localization by increasing the ITD range and b) improves elevational sound localization in the frontal field by introducing a shift of iso-ILD lines out of the midsagittal plane, which causes ILDs to increase with increasing stimulus elevation. The changes at the behavioral level could be related to the changes in the binaural physical parameters that occurred after the virtual removal of the ruff. These data provide new insights into the function of external hearing structures and open up the possibility to apply the results on autonomous agents, creation of virtual auditory environments for humans, or in hearing aids.
Correlating Molecular Phylogeny with Venom Apparatus Occurrence in Panamic Auger Snails (Terebridae):
Central to the discovery of neuroactive compounds produced by predatory marine snails of the superfamily Conoidea (cone snails, terebrids, and turrids) is identifying those species with a venom apparatus. Previous analyses of western Pacific terebrid specimens has shown that some Terebridae groups have secondarily lost their venom apparatus. In order to efficiently characterize terebrid toxins, it is essential to devise a key for identifying which species have a venom apparatus. The findings presented here integrate molecular phylogeny and the evolution of character traits to infer the presence or absence of the venom apparatus in the Terebridae. Using a combined dataset of 156 western and 33 eastern Pacific terebrid samples, a phylogenetic tree was constructed based on analyses of 16S, COI and 12S mitochondrial genes. The 33 eastern Pacific specimens analyzed represent four different species: Acus strigatus, Terebra argyosia, T. ornata, and T. cf. formosa. Anatomical analysis was congruent with molecular characters, confirming that species included in the clade Acus do not have a venom apparatus, while those in the clade Terebra do. Discovery of the association between terebrid molecular phylogeny and the occurrence of a venom apparatus provides a useful tool for effectively identifying the terebrid lineages that may be investigated for novel pharmacological active neurotoxins, enhancing conservation of this important resource, while providing supplementary information towards understanding terebrid evolutionary diversification.
Effect before Cause: Supramodal Recalibration of Sensorimotor Timing:
Our motor actions normally generate sensory events, but how do we know which events were self generated and which have external causes? Here we use temporal adaptation to investigate the processing stage and generality of our sensorimotor timing estimates. Adaptation to artificially-induced delays between action and event can produce a startling percept--upon removal of the delay it feels as if the sensory event precedes its causative action. This temporal recalibration of action and event occurs in a quantitatively similar manner across the sensory modalities. Critically, it is robust to the replacement of one sense during the adaptation phase with another sense during the test judgment. Our findings suggest a high-level, supramodal recalibration mechanism. The effects are well described by a simple model which attempts to preserve the expected synchrony between action and event, but only when causality indicates it is reasonable to do so. We further demonstrate that this model successfully characterises related adaptation data from outside the sensorimotor domain.
Visual Properties of Transgenic Rats Harboring the Channelrhodopsin-2 Gene Regulated by the Thy-1.2 Promoter:
Channelrhodopsin-2 (ChR2), one of the archea-type rhodopsins from green algae, is a potentially useful optogenetic tool for restoring vision in patients with photoreceptor degeneration, such as retinitis pigmentosa. If the ChR2 gene is transferred to retinal ganglion cells (RGCs), which send visual information to the brain, the RGCs may be repurposed to act as photoreceptors. In this study, by using a transgenic rat expressing ChR2 specifically in the RGCs under the regulation of a Thy-1.2 promoter, we tested the possibility that direct photoactivation of RGCs could restore effective vision. Although the contrast sensitivities of the optomotor responses of transgenic rats were similar to those observed in the wild-type rats, they were enhanced for visual stimuli of low-spatial frequency after the degeneration of native photoreceptors. This result suggests that the visual signals derived from the ChR2-expressing RGCs were reinterpreted by the brain to form behavior-related vision.
A Decade Later, How Much of Rwanda's Musculoskeletal Impairment Is Caused by the War in 1994 and by Related Violence?:
In 1994 there was a horrific genocide in Rwanda following years of tension, resulting in the murder of at least 800,000 people. Although many people were injured in addition to those killed, no attempt has been made to assess the lasting burden of physical injuries related to these events. The aim of this study was to estimate the current burden of musculoskeletal impairment (MSI) attributable to the 1994 war and related violence. A national cross-sectional survey of MSI was conducted in Rwanda. 105 clusters of 80 people were selected through probability proportionate to size sampling. Households within clusters were selected through compact segment sampling. Enumerated people answered a seven-question screening test to assess whether they might have an MSI. Those who were classed as potential cases in the screening test were examined and interviewed by a physiotherapist, using a standard protocol that recorded the site, nature, cause, and severity of the MSI. People with MSI due to trauma were asked whether this trauma occurred during the 1990-1994 war or during the episodes that preceded or followed this war. Out of 8,368 people enumerated, 6,757 were available for screening and examination (80.8%). 352 people were diagnosed with an MSI (prevalence = 5.2%, 95% CI = 4.5-5.9%). 106 cases of MSI (30.6%) were classified as resulting from trauma, based on self-report and the physiotherapist's assessment. Of these, 14 people (13.2%) reported that their trauma-related MSI occurred during the 1990-1994 war, and a further 7 (6.6%) that their trauma-related MSI occurred during the violent episodes that preceded and followed the war, giving an overall prevalence of trauma-related MSI related to the 1990-1994 war of 0.3% (95% CI = 0.2-0.4%). A decade on, the overall prevalence of MSI was relatively high in Rwanda but few cases appeared to be the result of the 1994 war or related violence.
Posted by Coturnix at 8:19 AM • 0 Comments • 0 TrackBacks
Category: Clock Quotes
If we had no winter, the spring would not be so pleasant; if we did not sometimes taste of adversity, prosperity would not be so welcome.
- Anne Dudley Bradstreet
Posted by Coturnix at 4:18 AM • 4 Comments • 0 TrackBacks
November 4, 2009
Category: North Carolina • Personal
Last night we went to see Leonard Cohen at the DPAC in Durham. What to say? He's the Legend. Still, at this age, full of energy and spunk. And everything was done to perfection - the set, the lighting and the slow dance of the backup singers had, together, a hypnotic effect. Three hours passed like nothing - I could have stayed another three (and that would still not exhaust all of his greatest hits).
I was too far away to take good pictures with my iPhone, but I took these two, just to show the light changes. There were some quite magical light effects as some moments including those making Leonard look green like a leprechaun.
I grew up with his music and it seems strange that some of his big hits, now 20 or 30 years old were once new - I knew them when they were new, buying his latest album and playing it over and over until I knew every note and every word. So long ago. I feel so old now.
Not that I was old compared to the rest of the audience there - lots of old hippies with gray beards and ponytails... ;-) After all, I was a teenager when I was crazy about Leonard and bought all his records, back in the 80s.
One weird thing .... I felt selfish last night. I did not want to share Cohen with thousands of others. I wanted to have him and the band all for myself. Just like back in the old days, when everyone is gone after the party, and only a handful of best friends remain for the night (the last bus is gone), a nice drink is taken out of hiding to replace the cheap party beer, incense is lit, and Cohen is on the gramophone. His music is for intimate occasions like that, in my mind, according to my memories and associations....
But I was happy nonetheless to finally see him sing live. After all these decades. Would not have missed it for anything. It was a magical night.
Posted by Coturnix at 10:10 PM • 3 Comments • 0 TrackBacks
Category: A Picture Is Worth A Thousand Words • Fun • North Carolina • Personal
The neighbors in Southern Village (here in Chapel Hill) are wild about Halloween, many making elaborate decorations of their houses for it (often more elaborate than for Christmas). The business on The Green also get into the spirit and put fun and scary dolls or scarecrows or other objects in front of their stores. These are often quite well designed as well. This year, we really liked this sign-post, showing the way to other businesses (e.g., Lumina Theater, Weaver Street Market, Harrington Bank, etc.) - click on buttons to see large:
Posted by Coturnix at 9:24 PM • 0 Comments • 0 TrackBacks
Category: Genetics • North Carolina • Science Education
Dog Genome: Teaching Scientists New Tricks
November 17th; 6:30-8:30 pm with discussion beginning at 7:00 followed by Q&A
The Irregardless Café, 901 W. Morgan Street, Raleigh 919.833.8898
This year, roughly 66,000 people will be diagnosed with non-Hodgkin lymphoma, while another 22,000 will be diagnosed with cancers of the brain. In parallel, our pet dogs also suffer from a range of similar spontaneous cancers. For thousands of years, humans and dogs have shared a unique bond--breathing the same air, drinking the same water, and living in the same environment. During the 21st century this relationship is now strengthened into one that may hold intriguing biomedical possibilities. Using the 'One Medicine' concept--the idea that human and animal health relies on a common pool of medical and scientific knowledge and is supported by overlapping technologies and discoveries; research is revealing that the dog genome may hold the keys to unlocking some of nature's most intriguing puzzles about human cancer.
About the Speaker: Dr. Matthew Breen, professor of genomics in the NC State University College of Veterinary Medicine, co-directs the Clinical Genomics Core of the Center for Comparative Medicine and Translational Research at NC State. Dr. Breen's lab http://www.breenlab.org/ helped map the canine genome in 2004 and the internationally known research scientist has conducted studies and published articles on numerous comparative medicine investigations of canine and human cancers including non-Hodgkin lymphoma, meningioma, and other cancers of the brain. A member of the Cancer Genetics Program at the University of North Carolina's Lineberger Comprehensive Cancer Center, Dr. Breen's collaborative investigations involve Duke University Medical Center and the University of Minnesota Medical Center among others.
RSVP: katey.ahmann@ncdenr.gov; or call 919-733-7450 ext 531
Posted by Coturnix at 1:16 PM • 0 Comments • 0 TrackBacks
Category: SO'10
As you know you can see everyone who's registered for the conference, but I highlight 4-6 participants every day as this may be an easier way for you to digest the list. You can also look at the Program so see who is doing what.
Dorothea Salo is an academic librarian in Wisconsin who blogs on The Book of Trogool. She tweets as well. At the conference, Dorothea will co-moderate the session "Scientists! What can your librarian do for you?" and teach a workshop "Repositories for Fun and Profit".
Peter Lipson is a physician in Michigan. He blogs on White Coat Underground and Science-Based Medicine and tweets. At the conference, Peter will co-moderate the session "Privacy, ethics, and disasters: how being online as a doctor changes everything" and teach a workshop ""Podcasting 101".
Anne Jeffersonis an assistant professor of geology at the University of North Carolina at Charlotte - she blogs on Highly Allochthonous. At the conference, Anne will co-moderate the session "Casting a wider net: Promoting gender and ethnic diversity in STEM".
James Hrynyshyn is a freelance science journalist in Saluda, in western North Carolina. He blogs on Island of Doubt and appears to be on Twitter as well.
Suzanne Franks, engineer and femininst better known online as Zuska, is another veteran of these conferences. Her blog is Thus Spake Zuska.
Posted by Coturnix at 11:44 AM • 0 Comments • 0 TrackBacks
Category: Carnivals
Circus of the Spineless #44 is up on Marmorkrebs blog
Posted by Coturnix at 11:14 AM • 0 Comments • 0 TrackBacks
Category: Science News
There are 14 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week - you go and look for your own favourites:
Experience Matters: Females Use Smell to Select Experienced Males for Paternal Care:
Mate choice and mating preferences often rely on the information content of signals exchanged between potential partners. In species where a female's reproduction is the terminal event in life it is to be expected that females choose high quality males and assess males using some honest indicator of male quality. The Nereidid polychaete, Neanthes acuminata, exhibits monogamous pairing and the release of eggs by females terminates her life and larval success relies entirely on a male's ability to provide paternal care. As such females should have developed reliable, condition-dependent criteria to choose mates to guarantee survival and care for offspring. We show that females actively chose males experienced in fatherhood over others. In the absence of experienced males dominance, as evident from male-male fights, is utilized for mate selection. The preference for experienced males is not affected by previous social interactions between the individuals. We show that the choice of the partner is based on chemical signals demonstrating a 'scent of experience' to females providing evidence for the role of chemical signals in sexual selection for paternal care adding to our understanding of the mechanisms regulating condition-dependent mate choice.
Why Amphibians Are More Sensitive than Mammals to Xenobiotics:
Dramatic declines in amphibian populations have been described all over the world since the 1980s. The evidence that the sensitivity to environmental threats is greater in amphibians than in mammals has been generally linked to the observation that amphibians are characterized by a rather permeable skin. Nevertheless, a numerical comparison of data of percutaneous (through the skin) passage between amphibians and mammals is lacking. Therefore, in this investigation we have measured the percutaneous passage of two test molecules (mannitol and antipyrine) and three heavily used herbicides (atrazine, paraquat and glyphosate) in the skin of the frog Rana esculenta (amphibians) and of the pig ear (mammals), by using the same experimental protocol and a simple apparatus which minimizes the edge effect, occurring when the tissue is clamped in the usually used experimental device.
The percutaneous passage (P) of each substance is much greater in frog than in pig. LogP is linearly related to logKow (logarithm of the octanol-water partition coefficient). The measured P value of atrazine was about 134 times larger than that of glyphosate in frog skin, but only 12 times in pig ear skin. The FoD value (Pfrog/Ppig) was 302 for atrazine, 120 for antipyrine, 66 for mannitol, 29 for paraquat, and 26 for glyphosate.
The differences in structure and composition of the skin between amphibians and mammals are discussed.
Chimerism in Wild Adult Populations of the Broadcast Spawning Coral Acropora millepora on the Great Barrier Reef:
Chimeras are organisms containing tissues or cells of two or more genetically distinct individuals, and are known to exist in at least nine phyla of protists, plants, and animals. Although widespread and common in marine invertebrates, the extent of chimerism in wild populations of reef corals is unknown. The extent of chimerism was explored within two populations of a common coral, Acropora millepora, on the Great Barrier Reef, Australia, by using up to 12 polymorphic DNA microsatellite loci. At least 2% and 5% of Magnetic Island and Pelorus Island populations of A. millepora, respectively, were found to be chimeras (3% overall), based on conservative estimates. A slightly less conservative estimate indicated that 5% of colonies in each population were chimeras. These values are likely to be vast underestimates of the true extent of chimerism, as our sampling protocol was restricted to a maximum of eight branches per colony, while most colonies consist of hundreds of branches. Genotypes within chimeric corals showed high relatedness, indicating that genetic similarity is a prerequisite for long-term acceptance of non-self genotypes within coral colonies. While some brooding corals have been shown to form genetic chimeras in their early life history stages under experimental conditions, this study provides the first genetic evidence of the occurrence of coral chimeras in the wild and of chimerism in a broadcast spawning species. We hypothesize that chimerism is more widespread in corals than previously thought, and suggest that this has important implications for their resilience, potentially enhancing their capacity to compete for space and respond to stressors such as pathogen infection.
Posted by Coturnix at 9:01 AM • 0 Comments • 0 TrackBacks
Category: Clock Quotes
I think that anyone who comes upon a Nautilus machine suddenly will agree with me that its prototype was clearly invented at some time in history when torture was considered a reasonable alternative to diplomacy.
- Anna Quindlin
Posted by Coturnix at 4:02 AM • 0 Comments • 0 TrackBacks
November 3, 2009
Category: SO'10
As you know you can see everyone who's registered for the conference, but I highlight 4-6 participants every day as this may be an easier way for you to digest the list. You can also look at the Program so see who is doing what.
Sheril Kirshenbaum is a good friend, a marine biologist and a former SciBling. She blogs at The Intersection, has co-authored "Unscientific America" and written the forthcoming "The Science of Kissing". After proclaiming she'd never do it, she succumbed to Twitter as well. At the conference, Sheril will co-moderate the session "Online Civility and Its (Muppethugging) Discontents".
Karen James is a postdoc in the Department of Botany at the Natural History Museum in London, UK. Another veteran of our conferences, Karen is the force behind the Beagle Project. She blogs on the Beagle Project Blog and her own Data Not Shown blog and is a force on Twitter. At the conference, Karen will co-moderate the session "Broader Impact Done Right" and demo the "Darwin and the Adventure - The (i)Movie".
Ashley Sue Allen, formerly the Community Content Liaison at NBC 17 ~ WNCN, is a writer and editor who now blogs on Green Grounded and Lumineux! and is on Twitter.
Xan Gregg, another veteran of our conferences, works in the JMP scientific statistical software division at SAS and writes a great blog about scientific visualization FORTH GO. And he can be found on Twitter (perhaps the conference will make him more active there!) as well.
Roger Harris is an independent social communications consultant and certainly has an interesting life story, combining science, writing, adventure and the Web. He has recently gone solo, with his Harris Social Media, blogs on TwitterThoughts and, as you can expect, tweets.
Posted by Coturnix at 12:19 PM • 2 Comments • 0 TrackBacks
Category: Carnivals
November edition of Scientia Pro Publica is up on Observations of a Nerd
Carnival Of Evolution, 17th Edition is up on Adaptive Complexity
Grand Rounds Vol. 6 No. 6 are up on Non-Clinic Jobs
Posted by Coturnix at 11:20 AM • 0 Comments • 0 TrackBacks
Category: Science News
New this morning in PLoS ONE, PLoS Biology and PLoS Medicine. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers:
Mandatory Disclosure of Pharmaceutical Industry-Funded Events for Health Professionals:
We are in a period of unprecedented scrutiny of the relationships between the pharmaceutical industry and doctors [1]-[4]. Legislators are now considering how they might become involved in the regulation of these practices. This is a telling comment on the perceived failure of the medical profession to regulate itself and of self-regulation by industry. But reliable and comprehensive data on the nature and extent of industry sponsorship are rare. Several states in the US have mandatory disclosure laws for physician payments, but these data have proved difficult to access and analyse [5]. The US Congress is considering new mechanisms for revealing industry-professional interactions (the so-called "Sunshine" Acts) [6],[7]...
Somatosensory Cortices Are Required for the Acquisition of Morphine-Induced Conditioned Place Preference:
Sensory system information is thought to play an important role in drug addiction related responses. However, how somatic sensory information participates in the drug related behaviors is still unclear. Many studies demonstrated that drug addiction represents a pathological usurpation of neural mechanisms of learning and memory that normally relate to the pursuit of rewards. Thus, elucidate the role of somatic sensory in drug related learning and memory is of particular importance to understand the neurobiological mechanisms of drug addiction. In the present study, we investigated the role of somatosensory system in reward-related associative learning using the conditioned place preference model. Lesions were made in somatosensory cortices either before or after conditioning training. We found that lesion of somatosensory cortices before, rather than after morphine conditioning impaired the acquisition of place preference. These results demonstrate that somatosensory cortices are necessary for the acquisition but not retention of morphine induced place preference.
Evolutionary History of the HAP2/GCS1 Gene and Sexual Reproduction in Metazoans:
The HAP2/GCS1 gene first appeared in the common ancestor of plants, animals, and protists, and is required in the male gamete for fusion to the female gamete in the unicellular organisms Chlamydomonas and Plasmodium. We have identified a HAP2/GCS1 gene in the genome sequence of the sponge Amphimedon queenslandica. This finding provides a continuous evolutionary history of HAP2/GCS1 from unicellular organisms into the metazoan lineage. Divergent versions of the HAP2/GCS1 gene are also present in the genomes of some but not all arthropods. By examining the expression of the HAP2/GCS1 gene in the cnidarian Hydra, we have found the first evidence supporting the hypothesis that HAP2/GCS1 was used for male gamete fusion in the ancestor of extant metazoans and that it retains that function in modern cnidarians.
A Simple Rule for Proteins to Follow:
Proteins are the workhorses of cells, acting as enzymes, structural elements, and signal transducers. The tremendous variability in proteins' chemical and physical properties is achieved through the manner in which they are made--by the mixing and matching of a set of basic building blocks known as amino acids. Each amino acid consists of a carbon atom attached to an amine group, a carboxyl group, a hydrogen atom, and one of 22 structurally and chemically distinct side groups. When a cell builds a protein, it uses the instructions encoded in a corresponding gene to tell it which amino acids to use, and in what order. A new protein is assembled front-to-back, with each new amino acid added to the growing chain by hooking its amine group to the carboxyl group of the previous amino acid...
An Integrated Analysis of Molecular Acclimation to High Light in the Marine Diatom Phaeodactylum tricornutum:
Photosynthetic diatoms are exposed to rapid and unpredictable changes in irradiance and spectral quality, and must be able to acclimate their light harvesting systems to varying light conditions. Molecular mechanisms behind light acclimation in diatoms are largely unknown. We set out to investigate the mechanisms of high light acclimation in Phaeodactylum tricornutum using an integrated approach involving global transcriptional profiling, metabolite profiling and variable fluorescence technique. Algae cultures were acclimated to low light (LL), after which the cultures were transferred to high light (HL). Molecular, metabolic and physiological responses were studied at time points 0.5 h, 3 h, 6 h, 12 h, 24 h and 48 h after transfer to HL conditions. The integrated results indicate that the acclimation mechanisms in diatoms can be divided into an initial response phase (0-0.5 h), an intermediate acclimation phase (3-12 h) and a late acclimation phase (12-48 h). The initial phase is recognized by strong and rapid regulation of genes encoding proteins involved in photosynthesis, pigment metabolism and reactive oxygen species (ROS) scavenging systems. A significant increase in light protecting metabolites occur together with the induction of transcriptional processes involved in protection of cellular structures at this early phase. During the following phases, the metabolite profiling display a pronounced decrease in light harvesting pigments, whereas the variable fluorescence measurements show that the photosynthetic capacity increases strongly during the late acclimation phase. We show that P. tricornutum is capable of swift and efficient execution of photoprotective mechanisms, followed by changes in the composition of the photosynthetic machinery that enable the diatoms to utilize the excess energy available in HL. Central molecular players in light protection and acclimation to high irradiance have been identified.
Posted by Coturnix at 11:09 AM • 0 Comments • 0 TrackBacks
Category: Clock Quotes
I was always looking outside myself for strength and confidence but it comes from within. It is there all the time.
- Anna Freud
Posted by Coturnix at 3:56 AM • 0 Comments • 0 TrackBacks
November 2, 2009
Category: Blogging • PLoS • Paleontology
...for October can be found here.
Posted by Coturnix at 4:37 PM • 0 Comments • 0 TrackBacks
Category: SO'10
As you know you can see everyone who's registered for the conference, but I highlight 4-6 participants every day as this may be an easier way for you to digest the list. You can also look at the Program so see who is doing what.
Trevor Owens is the community lead for the Zotero project at the Center for History and New Media and a doctoral student in the Graduate School of Education at George Mason University. He blogs at the eponimous blog and tweets.
At the conference, Trevor will do an Ignite-style talk "Data mining the literature with Zotero" and will participate in the session about "Online Reference Managers".
Marjee Chmiel (btw, Trevor and Marjee are married to each other) is a designer and producer of science video games at National Geographic's JASON Project. She is a PhD student in Instructional Technology at George Mason University, blogs at Science Games By Marjee and can also be found on Twitter.
At the conference, Marjee will do a demo of the JASON Project.
Russ Campbell is the communications officer for the Burroughs Wellcome Fund and the North Carolina Science, Mathematics and Technology Education Center. He is one of the co-founders of SCONC, blogs on the Science journalism Blog as well as on his personal blog Fishtown University.
He can also be found on Twitter and I interviewed him a few months ago.
Patric Lane is the Health and Science Editor at UNC News.
And yes, he tweets, too.
Jennifer Weston is the Director of Communication in the College of Engineering at NC State University who is also on Twitter.
Posted by Coturnix at 11:36 AM • 0 Comments • 0 TrackBacks
Category: Blogging
Go say Hello to Andrew Gelman at Applied Statistics.
You can check out the archives of his old blog here.
Posted by Coturnix at 10:14 AM • 2 Comments • 0 TrackBacks
Category: Clock Quotes
One act of beneficence, one act of real usefulness, is worth all the abstract sentiment in the world.
- Ann Radcliffe
Posted by Coturnix at 3:52 AM • 0 Comments • 0 TrackBacks
November 1, 2009
Category: Tweetlinks
Follow me on Twitter to get these, and more, in something closer to Real Time (all my tweets are also imported into FriendFeed where they are much more easy to search and comment on, as well as into my Facebook wall where they are seen by quite a different set of people):
Doctors' Lack of Respect Weighs on the Obese
Frogs in Boiling but Confusing Water: A Review of Climate Cover-Up
List of cognitive biases
Top Twitter Lists are very male...let's make a women-in-STEM and/or women-bloggers lists and such and push them.
A room of her own - 'Incredible story about a teacher who left a student $75K'
From sanctuary to snake pit: the rise and fall of asylums
The History of Birth Control
Posted by Coturnix at 7:36 PM • 0 Comments • 0 TrackBacks
Category: Carnivals
Berry Go Round #21 is up on Beetles In The Bush
Carnival of the Liberals #98: The Halloween Fearmongering Edition is up on Greta Christina's blog.
Posted by Coturnix at 4:07 PM • 0 Comments • 0 TrackBacks
Category: Housekeeping
October was a very busy month and the blog must have felt a little neglected. Still, I managed to post 142 times last month...and not just Clock Quotes.
Open Access Week was in October, and I particularly paid attention to Open Access Week in Serbia.
I announced the PLoS ONE Blog Pick of the Month for September 2009 , the new Genomics of Emerging Infectious Disease PLoS Collection and the New and Exciting in PLoS ONE - articles with embedded interactive 3D structures.
I got off the computer, out of the house and in the car and went to some science/technology local sites and events, which I blogged about in Field Trip! Water, sewage and flowers and New jobs in North Carolina at CREE, producing LED lights.
The big job last month for us was managing the registration for ScienceOnline2010. Within three days of opening for registration we had to close as we were full. Then I had to put together the final program Schedule.
You can hear more about ScienceOnline2010 On Duke Radio. And I started introducing the participants here, here, here, here and here.
Nothing raises the excitement about ScienceOnline2010 as much as reading the interviews with participants of ScienceOnline09. In October, I added four more interviews - with Arikia Millikan, Tatjana Jovanovic-Grove, Blake Stacey and Daniel Brown.
Being busy, instead of writing I posted a bunch of really cool videos - see The Piano Stairway, Plastic in the Pacific Gyre can be microscopic and never biodegrade, Why does plastic accumulate in the North Pacific Gyre?, It's so easy to re-use Open Access stuff, Open Access 101 (video), Teslapunk Antique Toilet of the Future, 500,000 Brazilian free-tailed bats fly out of a cave and Video of Anne Frank Surfaces on YouTube.
And I collected good links on Twitter and posted the best of them here in daily Tweetlinks.
Posted by Coturnix at 3:29 PM • 0 Comments • 0 TrackBacks
Category: SO'10
If you are coming to ScienceOnline2010 and you have checked the amazing Program there, you have noticed that there will be a set of hands-on workshops on Friday morning.
If you will be attending, you can sign up for workshops now - one 10am and one 11am worskhop. How do you sign up? By editing the Workshops page of the wiki - just add the number (up to 50 per session) and your name under the titles of workshops you want to participate in.
How do you choose which two workshops to attend?
If you want to start a blog and don't know how, sign up for Blogging 101 and an hour later you will have your own blog, ready to fill with content of your own, perhaps starting with your coverage of the conference over those three days.
If you already write a blog, but want to make your blog better, prettier, more interesting, more functional and, importantly, less isolated, i.e., better connected to the rest of the Web, sign up for Blogging 102.
If running a single, personal blog is not your thing (or you've already been doing it for years) and you are ready to step up and design your own site, something more complex and more flexible, with news, podcasts, videos, perhaps multiple blogs written by multiple users, then it may be time to start getting familiar with Drupal (yes, even the White House is now using Drupal for its sites). Get started in the Make your own social networking site with Drupal workshop.
Scientific articles get deposited into mysterious online places called Library Repositories. What are those? How do you use them? How do you find information in them? If you publish a paper, how do you deposit it there? This will all be answered in the Repositories for Fun and Profit session.
Sick of searching the Web for other people's images to use in your blog posts? Make your own. Learn how to use easy artistic and graphic tools in the Paint your blog images using a digital tablet session (watch that page - you may be asked to download software ahead of time).
Everyone can point a Flip camera and shoot, then upload the file on YouTube, right? Yes, but there are things to know and tricks to use to make your videos much better, thus more interesting, useful and educational. Learn the basics of Storyboarding your science video and posting it online.
Twitter, FriendFeed, Facebook, Flickr, YouTube, Stumbleupon....you have heard of all of these and other social networking sites. But you are not on them and don't know how to use them. Or you are on them, but not really sure how to use them. Perhaps all you give and get there is silly and useless stuff. How do you find science information and/or other scientists on these services, how do you use those services to exchange useful information, to collaborate, or promote your organization? Find out in the Social media for beginners workshop.
Perhaps sound is your thing, rather than writing, images and video. Learn how to record and upload audio files and how to make them good, fun and useful in the Podcasting 101 session.
You can ask questions of the workshop leaders on their individual pages. Start signing up now.
Posted by Coturnix at 12:19 PM • 0 Comments • 0 TrackBacks
Category: Clock Quotes
Lost time is like a run in a stocking. It always gets worse.
- Ann Morrow Lindbergh
Posted by Coturnix at 3:44 AM • 0 Comments • 0 TrackBacks
Category: Tweetlinks
Follow me on Twitter to get these, and more, in something closer to Real Time (all my tweets are also imported into FriendFeed where they are much more easy to search and comment on, as well as into my Facebook wall where they are seen by quite a different set of people):
Every plastic bag and bottle you've ever used still exists
Deal in Senate on Protecting News Sources
Are you a 'messy thinker'?
The Complete Guide to Google Wave
Found one of these today. Obviously written by a coward. Boo!
A Must-Read for journos: There may be a future for the news business, but it's going to be unrecognizable: We Just Don't Know: An Interview with Jonathan Glick - "It was the monopoly that created the journalism, not the journalism that created the monopoly."
A Must-Read for journos: Narrative is dead! Long live Narrative!
A Must-Read for journos: Toward post-Journalism journalism
A Must-Read for journos: Wild guesses won't solve journalism crisis
Another Must-Read for journos: The Only 'Journalism' Subsidy We Need is in Bandwidth
Constraining America's Brightest
Global/national and hyperlocal papers will thrive, metros will die, I always say. Perhaps I'm right:Most national papers in America are faring better than metropolitan ones
Global warming is not a liberal issue. GW Denialism is a conservative issue, though: Do two reporters have a conflict on the beat? - Equal voice=dereliction of journo duty.
For The Future Of The Media Industry, Look In The App Store
Posted by Coturnix at 12:35 AM • 0 Comments • 0 TrackBacks
October 31, 2009
Category: Clock Quotes
We barely have time to react in this world, let alone rehearse.
- Ani Difranco
Posted by Coturnix at 4:00 AM • 0 Comments • 0 TrackBacks
Category: Carnivals
Scientia Pro Publica #14 is up on Genetic Inference
Friday Ark #267 is up on Modulator
Posted by Coturnix at 12:11 AM • 0 Comments • 0 TrackBacks
