ScienceOnline2010 session videos – Science and Entertainment Part 6

Science and Entertainment: Beyond Blogging
Saturday, January 16 at 2 – 3:05pm
D. Science and Entertainment: Beyond Blogging – Tamara Krinsky and Jennifer Ouellette
Description: Over the past several years, the Internet has tangibly changed the way that movies and TV shows are produced and marketed. Blogs will call out ridiculous scientific errors found in stories and the critique can go viral very quickly; therefore, science advising is on the rise in an attempt to add some semblance of plausibility to your favorite flicks. As tools on the web continue to evolve, filmmakers and television creators are finding new ways to connect with and market to their viewers. For some shows, this has meant tapping into the science featured in their content, ranging from an exploration of the roots of the science that has been fictionalized to the expansion of a scientific topic explored in a documentary. In this session, we’ll look at how online video and social networking tools are playing a part in connecting science, Hollywood and its fans.

Today’s carnivals

The new Change of Shift is up on mamatrauma
Friday Ark #285 is up on Modulator

New and Exciting in PLoS ONE

There are 19 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:
Winter Active Bumblebees (Bombus terrestris) Achieve High Foraging Rates in Urban Britain:

Foraging bumblebees are normally associated with spring and summer in northern Europe. However, there have been sightings of the bumblebee Bombus terrestris during the warmer winters in recent years in southern England. But what floral resources are they relying upon during winter and how much winter forage can they collect? To test if urban areas in the UK provide a rich foraging niche for bees we set up colonies of B. terrestris in the field during two late winter periods (2005/6 & 2006/7) in London, UK, and measured their foraging performance. Fully automatic radio-frequency identification (RFID) technology was used in 2006/7 to enable us to record the complete foraging activity of individually tagged bees. The number of bumblebees present during winter (October 2007 to March 2008) and the main plants they visited were also recorded during transect walks. Queens and workers were observed throughout the winter, suggesting a second generation of bee colonies active during the winter months. Mass flowering shrubs such as Mahonia spp. were identified as important food resources. The foraging experiments showed that bees active during the winter can attain nectar and pollen foraging rates that match, and even surpass, those recorded during summer. B. terrestris in the UK are now able to utilise a rich winter foraging resource in urban parks and gardens that might at present still be under-exploited, opening up the possibility of further changes in pollinator phenology.

Microarrays Reveal Early Transcriptional Events during the Termination of Larval Diapause in Natural Populations of the Mosquito, Wyeomyia smithii:

The mosquito Wyeomyia smithii overwinters in a larval diapause that is initiated, maintained and terminated by day length (photoperiod). We use a forward genetic approach to investigate transcriptional events involved in the termination of diapause following exposure to long-days. We incorporate a novel approach that compares two populations that differentially respond to a single day length. We identify 30 transcripts associated with differential response to day length. Most genes with a previously annotated function are consistent with their playing a role in the termination of diapause, in downstream developmental events, or in the transition from potentially oxygen-poor to oxygen-rich environments. One gene emerges from three separate forward genetic screens as a leading candidate for a gene contributing to the photoperiodic timing mechanism itself (photoperiodic switch). We name this gene photoperiodic response gene 1 (ppdrg1). WsPpdrg1 is up-regulated under long-day response conditions, is located under a QTL for critical photoperiod and is associated with critical photoperiod after 25 generations of recombination from a cross between extreme phenotypes. Three independent forward genetic approaches identify WsPpdrg1 as a gene either involved in the photoperiodic switch mechanism or very tightly linked to a gene that is. We conclude that continued forward genetic approaches will be central to understanding not only the molecular basis of photoperiodism and diapause, but also the evolutionary potential of temperate and polar animal populations when confronted with rapid climate change.

Year-Round Tracking of Small Trans-Saharan Migrants Using Light-Level Geolocators:

Since 1899 ringing (or banding) remained the most important source of information about migration routes, stopover sites and wintering grounds for birds that are too small to carry satellite-based tracking systems. Despite the large quantity of migrating birds ringed in their breeding areas in Europe, the number of ring recoveries from sub-Saharan Africa is very low and therefore the whereabouts of most small bird species outside the breeding season remain a mystery. With new miniaturized light-level geolocators it is now possible to look beyond the limits of ring recovery data. Here we show for the first time year round tracks of a near passerine trans-Saharan migrant, the European Hoopoe (Upupa epops epops). Three birds wintered in the Sahel zone of Western Africa where they remained stationary for most of the time. One bird chose a south-easterly route following the Italian peninsula. Birds from the same breeding population used different migration routes and wintering sites, suggesting a low level of migratory connectivity between breeding and wintering areas. Our tracking of a near passerine bird, the European Hoopoe, with light-level geolocators opens a new chapter in the research of Palaearctic-African bird migration as this new tool revolutionizes our ability to discover migration routes, stopover sites and wintering grounds of small birds.

Threatened Corals Provide Underexplored Microbial Habitats:

Contemporary in-depth sequencing of environmental samples has provided novel insights into microbial community structures, revealing that their diversity had been previously underestimated. Communities in marine environments are commonly composed of a few dominant taxa and a high number of taxonomically diverse, low-abundance organisms. However, studying the roles and genomic information of these “rare” organisms remains challenging, because little is known about their ecological niches and the environmental conditions to which they respond. Given the current threat to coral reef ecosystems, we investigated the potential of corals to provide highly specialized habitats for bacterial taxa including those that are rarely detected or absent in surrounding reef waters. The analysis of more than 350,000 small subunit ribosomal RNA (16S rRNA) sequence tags and almost 2,000 nearly full-length 16S rRNA gene sequences revealed that rare seawater biosphere members are highly abundant or even dominant in diverse Caribbean corals. Closely related corals (in the same genus/family) harbored similar bacterial communities. At higher taxonomic levels, however, the similarities of these communities did not correlate with the phylogenetic relationships among corals, opening novel questions about the evolutionary stability of coral-microbial associations. Large proportions of OTUs (28.7-49.1%) were unique to the coral species of origin. Analysis of the most dominant ribotypes suggests that many uncovered bacterial taxa exist in coral habitats and await future exploration. Our results indicate that coral species, and by extension other animal hosts, act as specialized habitats of otherwise rare microbes in marine ecosystems. Here, deep sequencing provided insights into coral microbiota at an unparalleled resolution and revealed that corals harbor many bacterial taxa previously not known. Given that two of the coral species investigated are listed as threatened under the U.S. Endangered Species Act, our results add an important microbial diversity-based perspective to the significance of conserving coral reefs.

Attribute Pair-Based Visual Recognition and Memory:

In the human visual system, different attributes of an object, such as shape, color, and motion, are processed separately in different areas of the brain. This raises a fundamental question of how are these attributes integrated to produce a unified perception and a specific response. This “binding problem” is computationally difficult because all attributes are assumed to be bound together to form a single object representation. However, there is no firm evidence to confirm that such representations exist for general objects. Here we propose a paired-attribute model in which cognitive processes are based on multiple representations of paired attributes. In line with the model’s prediction, we found that multiattribute stimuli can produce an illusory perception of a multiattribute object arising from erroneous integration of attribute pairs, implying that object recognition is based on parallel perception of paired attributes. Moreover, in a change-detection task, a feature change in a single attribute frequently caused an illusory perception of change in another attribute, suggesting that multiple pairs of attributes are stored in memory. The paired-attribute model can account for some novel illusions and controversial findings on binocular rivalry and short-term memory. Our results suggest that many cognitive processes are performed at the level of paired attributes rather than integrated objects, which greatly facilitates the binding problem and provides simpler solutions for it.

Clock Quotes

He is not only dull himself; he is the cause of dullness in others.
-Samuel Johnson

ScienceOnline2010 – interview with Andrew Farke

Continuing with the tradition from last two years, I will occasionally post interviews with some of the participants of the ScienceOnline2010 conference that was held in the Research Triangle Park, NC back in January. See all the interviews in this series here. You can check out previous years’ interviews as well: 2008 and 2009.
Today, I asked Andy Farke from the Raymond M. Alf Museum of Paleontology in Claremont, CA to answer a few questions.
Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your (scientific) background?
I grew up in rural South Dakota, with a high school graduating class of only 16 students. From a very young age, I had always been fascinated by paleontology (the study of past life, including dinosaurs). Because I didn’t know any better, I started writing to paleontologists whose names I found in some of my books, asking for assistance with little research projects that I had devised. One thing led to another, and the next thing I knew I was competing (and placing) in the Intel Science and Engineering Fair. (I feel just a twinge of personal pride over this, because I did rather well despite lacking access to the large research university labs and formal school programs that so many of my competitors had!) One of these projects led directly to my Ph.D. work at Stony Brook University, which I finished in 2008. Today, I’m a curator at Raymond M. Alf Museum of Paleontology in Claremont, California. Not only do I work as a researcher, but I’m also fortunate in that our museum is partnered with a high school (The Webb Schools), and many of the students from there are quite active in our museum’s research, outreach, and other activities. Because of my own experiences, I’m firmly convinced that science can be done by anyone, and that science should be accessible to everyone.
Tell us a little more about your career trajectory so far: interesting projects past and present?
A good portion of my career (indeed, beginning in high school) has been devoted to understanding the horned dinosaurs (Triceratops and their relatives). I’m particularly interested in how their massive skulls, measuring up to 3 meters in total length, functioned. Horned dinosaurs are odd, in that they have giant sinuses beneath the horns. Some researchers had speculated these sinuses functioned as shock absorbers during horn-to-horn combat, based on the observation that bighorn sheep and other modern horned animals also have big sinuses in their skulls. It turns out that we really don’t understand the sinuses even in modern animals – so many of my research efforts have focused on unraveling this problem. Other research projects have included describing and interpreting the evolutionary relationships of some new species of horned dinosaurs, paleopathology (the study of injury and disease in the fossil record), and the paleontology of Madagascar.
Andy Farke pic.jpg
What is taking up the most of your time and passion these days? What are your goals?
Right now, I’m working on advancing open science in my own field of paleontology. Open access publishing is certainly a part of this – I’m a volunteer section editor for paleontology at PLoS ONE. Paleontology is a science that relies heavily on lengthy descriptions and quality illustrations – but recent trends in science publishing mean that more and more of the “good stuff” is either consigned to effectively invisible supplemental information or just not published at all. It’s my hope that not only will electronic publications like PLoS ONE and Palaeontologia Electronica increase the exposure of our research, but that they will improve the quality of our research by allowing paleontologists to publish complete, well-illustrated descriptions of specimens from the start. Second, I’m a firm proponent of increasing data sharing and transparency. The vast majority of quantitative studies in paleontology quite frankly aren’t reproducible – the numbers behind the statistics are locked up on someone’s hard drive. With the ease of including supplemental information or depositing data in online archives, there is simply no excuse for this situation. So, I (along with several colleagues) am working on changing this attitude in our field.
What aspect of science communication and/or particular use of the Web in science interests you the most?
I think it’s really cool that it’s so easy to connect scientists with other scientists, and scientists with interested members of the general public. That’s part of the reason why Matt Wedel, Mike Taylor, and I founded the Open Dinosaur Project. In short, this project allows anyone with an internet connection (regardless of education, profession, or geographic location) to participate in dinosaur science. Our volunteers are helping us to amass a giant database of dinosaur limb bone measurements from the literature and museum specimens, which we’re analyzing to understand the evolution of dinosaur locomotion. Every aspect of the project is open – from data collection to publication. Our volunteers provide measurements, suggest analytical approaches, and much more. Most of the participants will be co-authors on the resulting paper!
How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, FriendFeed and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?
I blog at The Open Source Paleontologist as well as The Open Dinosaur Project. Through these blogs, I trade research techniques and philosophies with colleagues and try to advance the case for open science within our discipline. Blogging has been a great way to meet other researchers, developing friendships and collaborations that wouldn’t have happened otherwise. Facebook in particular is most widely used in paleo, and it’s proven to be useful for keeping up with everyone else’s research activities. There’s no doubt that all of this online activity is a huge positive.
When and how did you first discover science blogs? What are some of your favourites? Have you discovered any cool science blogs by the participants at the Conference?
I can honestly say that my earliest exposure to science blogs was through A Blog Around the Clock, and my reading list has ballooned since then. Among others, I always look forward to updates on Dave Hone’s Archosaur Musings, Sauropod Vertebra Picture of the Week, and Save Your Breath For Running Ponies (the funniest science blog, period). From ScienceOnline2010, I was happy to discover the blogs of Cameron Neylon, Jean-Claude Bradley, and Dorothea Salo, among others.
What was the best aspect of ScienceOnline2010 for you? Any suggestions for next year? Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?
My favorite part of ScienceOnline was getting to meet so many folks I had only heard of or communicated with through the Internet – people like Pete Binfield and Janet Stemwedel. Even better were those unexpected meetings with so many other open science advocates. I left the conference energized and excited about carrying on the push for open science!
It was so nice to see you again and thank you for the interview. I hope to see you again next January.

The Ecological and Economic Importance of Sharks, Threats They Face, and How You Can Help (CANCELLED)

From the NC Museum of Life Sciences:

Program Type: Science Talk
Date: Mar. 9, 7 pm – Mar. 9, 8 pm
Location: Museum of Natural Sciences – Auditorium
Fee: $6 General Public, $4 Members, $3 Students
The Ecological and Economic Importance of Sharks, Threats They Face, and How You Can Help
Lecture, slide show & video presentation by marine biologist David Shiffman
David Shiffman and friendShiffman graduated with distinction in Biology from Duke and is now a Masters in Marine Biology candidate at the College of Charleston in South Carolina. His research focuses on the feeding behavior and conservation of sandbar sharks. Shiffman is also a prolific writer for Southern Fried Science, one of the most widely read marine biology blogs on the internet.
Seating is limited. Reserve your seat now for this multimedia presentation by visiting or calling the Museum Box Office at 919.733.7450 x212. Fee: $6 for general public (discounts for Museum Members and Students).
The Museum’s current special exhibit, “Megalodon: Largest Shark that Ever Lived,” will be open from 5 to 7pm prior to the presentation. At 60 feet long and weighing nearly 100 tons, Carcharodon megalodon was the most powerful fish that ever lived and a dominant marine predator. While the Megalodon vanished 2 million years ago, its fascinating story continues to inspire lessons for contemporary science and shark conservation. “Megalodon” runs through May 9, 2010. Fee: $7 Adults; $5 Seniors/Students; $4 Children (5-11); free to Members.

ScienceOnline2010 session videos – Science and Entertainment Part 5

Science and Entertainment: Beyond Blogging
Saturday, January 16 at 2 – 3:05pm
D. Science and Entertainment: Beyond Blogging – Tamara Krinsky and Jennifer Ouellette
Description: Over the past several years, the Internet has tangibly changed the way that movies and TV shows are produced and marketed. Blogs will call out ridiculous scientific errors found in stories and the critique can go viral very quickly; therefore, science advising is on the rise in an attempt to add some semblance of plausibility to your favorite flicks. As tools on the web continue to evolve, filmmakers and television creators are finding new ways to connect with and market to their viewers. For some shows, this has meant tapping into the science featured in their content, ranging from an exploration of the roots of the science that has been fictionalized to the expansion of a scientific topic explored in a documentary. In this session, we’ll look at how online video and social networking tools are playing a part in connecting science, Hollywood and its fans.

New and Exciting in PLoS ONE

There are 27 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:
Body Size Evolution in Insular Speckled Rattlesnakes (Viperidae: Crotalus mitchellii):

Speckled rattlesnakes (Crotalus mitchellii) inhabit multiple islands off the coast of Baja California, Mexico. Two of the 14 known insular populations have been recognized as subspecies based primarily on body size divergence from putative mainland ancestral populations; however, a survey of body size variation from other islands occupied by these snakes has not been previously reported. We examined body size variation between island and mainland speckled rattlesnakes, and the relationship between body size and various island physical variables among 12 island populations. We also examined relative head size among giant, dwarfed, and mainland speckled rattlesnakes to determine whether allometric differences conformed to predictions of gape size (and indirectly body size) evolving in response to shifts in prey size. Insular speckled rattlesnakes show considerable variation in body size when compared to mainland source subspecies. In addition to previously known instances of gigantism on Ángel de la Guarda and dwarfism on El Muerto, various degrees of body size decrease have occurred frequently in this taxon, with dwarfed rattlesnakes occurring mostly on small, recently isolated, land-bridge islands. Regression models using the Akaike information criterion (AIC) showed that mean SVL of insular populations was most strongly correlated with island area, suggesting the influence of selection for different body size optima for islands of different size. Allometric differences in head size of giant and dwarf rattlesnakes revealed patterns consistent with shifts to larger and smaller prey, respectively. Our data provide the first example of a clear relationship between body size and island area in a squamate reptile species; among vertebrates this pattern has been previously documented in few insular mammals. This finding suggests that selection for body size is influenced by changes in community dynamics that are related to graded differences in area over what are otherwise similar bioclimatic conditions. We hypothesize that in this system shifts to larger prey, episodic saturation and depression of primary prey density, and predator release may have led to insular gigantism, and that shifts to smaller prey and increased reproductive efficiency in the presence of intense intraspecific competition may have led to insular dwarfism.

Beer Consumption Increases Human Attractiveness to Malaria Mosquitoes:

Malaria and alcohol consumption both represent major public health problems. Alcohol consumption is rising in developing countries and, as efforts to manage malaria are expanded, understanding the links between malaria and alcohol consumption becomes crucial. Our aim was to ascertain the effect of beer consumption on human attractiveness to malaria mosquitoes in semi field conditions in Burkina Faso. We used a Y tube-olfactometer designed to take advantage of the whole body odour (breath and skin emanations) as a stimulus to gauge human attractiveness to Anopheles gambiae (the primary African malaria vector) before and after volunteers consumed either beer (n = 25 volunteers and a total of 2500 mosquitoes tested) or water (n = 18 volunteers and a total of 1800 mosquitoes). Water consumption had no effect on human attractiveness to An. gambiae mosquitoes, but beer consumption increased volunteer attractiveness. Body odours of volunteers who consumed beer increased mosquito activation (proportion of mosquitoes engaging in take-off and up-wind flight) and orientation (proportion of mosquitoes flying towards volunteers’ odours). The level of exhaled carbon dioxide and body temperature had no effect on human attractiveness to mosquitoes. Despite individual volunteer variation, beer consumption consistently increased attractiveness to mosquitoes. These results suggest that beer consumption is a risk factor for malaria and needs to be integrated into public health policies for the design of control measures.

Periodic Table of Virus Capsids: Implications for Natural Selection and Design:

For survival, most natural viruses depend upon the existence of spherical capsids: protective shells of various sizes composed of protein subunits. So far, general evolutionary pressures shaping capsid design have remained elusive, even though an understanding of such properties may help in rationally impeding the virus life cycle and designing efficient nano-assemblies. This report uncovers an unprecedented and species-independent evolutionary pressure on virus capsids, based on the the notion that the simplest capsid designs (or those capsids with the lowest “hexamer complexity”, ) are the fittest, which was shown to be true for all available virus capsids. The theories result in a physically meaningful periodic table of virus capsids that uncovers strong and overarching evolutionary pressures, while also offering geometric explanations to other capsid properties (rigidity, pleomorphy, auxiliary requirements, etc.) that were previously considered to be unrelatable properties of the individual virus. Apart from describing a universal rule for virus capsid evolution, our work (especially the periodic table) provides a language with which highly diverse virus capsids, unified only by geometry, may be described and related to each other. Finally, the available virus structure databases and other published data reiterate the predicted geometry-derived rules, reinforcing the role of geometry in the natural selection and design of virus capsids.

Asymmetries in Perception of 3D Orientation:

Visual scene interpretation depends on assumptions based on the statistical regularities of the world. People have some preference for seeing ambiguously oriented objects (Necker cubes) as if tilted down or viewed from above. This bias is a near certainty in the first instant (~1 s) of viewing and declines over the course of many seconds. In addition, we found that there is modulation of perceived orientation that varies with position–for example objects on the left are more likely to be interpreted as viewed from the right. Therefore there is both a viewed-from-above prior and a scene position-dependent modulation of perceived 3-D orientation. These results are consistent with the idea that ambiguously oriented objects are initially assigned an orientation consistent with our experience of an asymmetric world in which objects most probably sit on surfaces below eye level.

Modeling Seasonal Influenza Outbreak in a Closed College Campus: Impact of Pre-Season Vaccination, In-Season Vaccination and Holidays/Breaks:

College and university students experience substantial morbidity from influenza and influenza-like illness, and they can benefit substantially from vaccination. Public health authorities encourage vaccination not only before the influenza season but also into and even throughout the influenza season. We conducted the present study to assess the impact of various vaccination strategies including delayed (i.e., in-season) vaccination on influenza outbreaks on a college campus. We used a Susceptible → Infected → Recovered (SIR) framework for our mathematical models to simulate influenza epidemics in a closed, college campus. We included both students and faculty/staff in the model and derived values for the model parameters from the published literature. The values for key model parameters were varied to assess the impact on the outbreak of various pre-season and delayed vaccination rates; one-way sensitivity analyses were conducted to test the sensitivity of the model outputs to changes in selected parameter values. In the base case, with a pre-season vaccination rate of 20%, no delayed vaccination, and 1 student index case, the total attack rate (total percent infected, TAR) was 45%. With higher pre-season vaccination rates TARs were lower. Even if vaccinations were given 30 days after outbreak onset, TARs were still lower than the TAR of 69% in the absence of vaccination. Varying the proportions of vaccinations given pre-season versus delayed until after the onset of the outbreak gave intermediate TAR values. Base case outputs were sensitive to changes in infectious contact rates and infectious periods and a holiday/break schedule. Delayed vaccination and holidays/breaks can be important adjunctive measures to complement traditional pre-season influenza vaccination for controlling and preventing influenza in a closed college campus.

Today’s carnivals

I and the Bird #120 is up on Sand creek almanac
Berry-Go-Round #25 is up on Foothills Fancies

Clock Quotes

Life is about enjoying yourself and having a good time.
– Cher

ScienceOnline2010 – interview with Mark MacAllister

Continuing with the tradition from last two years, I will occasionally post interviews with some of the participants of the ScienceOnline2010 conference that was held in the Research Triangle Park, NC back in January. See all the interviews in this series here. You can check out previous years’ interviews as well: 2008 and 2009.
Today, I asked Mark MacAllister, Coordinator of On-Line Learning Projects at the North Carolina Zoological Society to answer a few questions.
Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your (scientific) background?
Mark Macallister pic.JPGI was born and educated in the Midwest–grew up in northwest Illinois, spent a lot of time on my grandparents’ dairy farm in southwest Wisconsin, and went to undergrad school at Oberlin College. I then came south for the first of three tours of duty in North Carolina, including grad school at UNC-Chapel Hill. Also mixed in there is time spent living and working in Salt Lake City, St. Louis, Buffalo, Toronto, London and Chicago. I’m still a Midwesterner at heart, and really miss long sightlines and cold winters. But I love North Carolina, especially my current and quirky hometown of Pittsboro–it’s kind of like “The Andy Griffith Show” where every third person is a massage therapist. I work for the North Carolina Zoological Society, which is based in Asheboro, but telecommute from my shed-in-the-woods office in Pittsboro.
Philosophically, I tend to find myself most interested in the place where technology, education (especially K-12 but also for adults) and environmental advocacy come together. I feel that each one of those can be improved by the application of the other two–if that makes any sense. I’m an early adopter in all three, and have been lucky enough to be able to be involved in somewhat radically new things in each area. I’ve been self-teaching on computers since 1982, beginning with a Kaypro running CP/M. My Master’s degree is in Environmental Policy and Law, meaning that I took half my coursework in UNC’s Political Science department and the other half through the Law School. And, as far as teaching goes–one of the nicest compliments anyone ever paid me was to call me a “natural teacher,” meaning that I don’t have a teaching license but I somehow manage to pull it off.
Tell us a little more about your career trajectory so far: interesting projects past and present?
After grad school, my wife and I moved to Salt Lake City. I spent five years out there working on wilderness advocacy. I did a lot of research in the field–getting paid to hike and camp in the deserts of southern Utah was a great gig–and also in the public document rooms of various state and federal agencies. The advocacy groups I worked with were involved in mining, grazing, water rights, logging and other threats to wilderness preservation. What I began to notice toward the end of my tenure there was that many issues that appeared to be landscape-related were actually endangered species-related, and as a result I began to become more interested in species preservation.
We came back to North Carolina and in 1996 I went to work for the Chatham County Schools administrative office. The state was just beginning to wire classrooms, the Internet was just beginning to find its footing in terms of K-12 education, and Chatham understood early on that a significant teacher training effort would need to follow close on the heels of the effort to get everything wired. My job was in many ways focused on creating an atmosphere of support for integrating the Internet into classrooms; in other words, I was asked to help teachers understand why adopting technology was in everyone’s best interest, and then to work with them to actually help them gain those skills. Not long after we got started, Chatham was recognized as one of the ten top technology school districts in the country.
While this was all going on, I found myself thinking more and more about the content of the K-12 curriculum. It seemed obvious that a wonderful way to interest kids and meet curriculum goals was to focus the whole deal on the study of animals and wildlife, and to do so with technology-rich methods. I approached the Education Curator at the North Carolina Zoo, and not long after that we were partnering to build two websites focused on field-based wildlife research. These sites eventually evolved into FieldTripEarth, which is one of the many things I’m working on these days. I’ve been at the Zoo for ten years now, and have seen through a variety of other projects, ranging from teacher education (in both the US and Africa) to social media planning to field-based informal education.
What is taking up the most of your time and passion these days? What are your goals?
I’m often thinking about “raw learning materials” (this is David Warlick’s term, see Landmark Project) and how to best put them into the hands of students and teachers. I’m not particularly interested in curriculum–that is, in designing and assembling big packages of resources that teachers can then plug into their classrooms. Rather, I’m curious about how best to make original source material available to classrooms and, better yet, how to put those classrooms in contact with the people that actually generate those source materials (By source materials, I mean first-person narratives, photos, video, datasets, maps and so on that, taken together, tell a story about what a scientist or other field researcher is working on). FieldTripEarth wheels and deals in exactly this currency, and we’ve been successful in providing classrooms a way to access these materials from researchers working all over the world. What they do with them is, for the most part, up to the students and teachers–we do offer some generalized strategies for using the materials found on the website, but for the most part we urge everyone to apply them to meet their specific needs.
What I wish I could spend more time on–or at least be more successful at doing–is bringing various classrooms into substantive contact with each other. I don’t mean waving at each other through Skype…rather, what I’m on the lookout for are ways to help students in various locations work together to solve learning problems, to interview field scientists, to author a video about a particular topic, and so on. I think there’s a lot of potential in this, but I’m not convinced that teachers and administrators will buy into it.
More generally, I’m interested in teaching process and thinking skills to whoever will sit still long enough to learn them. What we commonly call the scientific method can of course be used to learn in any academic or technical area. Unfortunately, most schools aren’t teaching thinking as an organized process; that’s why I try to focus on the work being done by field researchers, because I consider them role models of sorts when it comes thinking that is both multi-disciplinary and systematic.
I have some other goals, of course. I’d like to figure out a way to make hiking and biking more a part of the K-12 classroom. I’d like to read and write more, and to think out loud with colleagues more frequently.
How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, FriendFeed and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?
I’ve never really taken to blogging as part of my work, though I do read several blogs focused on politics and policy, both of which are hobby horses of mine. Twitter and Facebook are a relatively small part of my professional life, mostly because right now my employer focuses more on their utility in serving members than in educating them. I think these tools form a net positive, but will be much more relevant once we figure out how to use them as educational, rather than informational, resources.
What was the best aspect of ScienceOnline2010 for you? Any suggestions for next year? Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?
The best thing about the conference was witnessing the various interests people brought with them–as well as the varying levels of expertise. It helped me remember that this is still such an evolving area. The sessions were all strong, but for the most part my strongest impressions were formed outside of the meeting rooms.
As far as suggestions for next year–it would be cool to invite some consumers of science communication and let us see how they put it to work in their lives. There was a bit of that at 2010, but there’s a lot of untapped experience out there.
And while we’re at it, I’d love to have a session focused on the question “How do we make our students’ experiences with technology at school at least as rich and relevant as the experiences they are having outside of school?”
It was so nice to meet you and thank you for the interview. I hope to see you again next January.

Science Cafe Raleigh – Our bodies: the Final Frontier

From the NC Museum of Natural Sciences:

OUR BODIES: The Final Frontier
Tuesday, March 23, 2010 – 6:30-8:30 pm with discussion beginning
at 7:00 followed by Q&A
Location: Tir Na Nog 218 South Blount Street, Raleigh, 833-7795
We have come to think of the world as known. It isn’t. Even basic parts of our own bodies remain totally unexplored. For example, have you ever stopped to wonder why you are naked? Aside from naked mole rats, we are among the only land mammals to be essentially devoid of hair. Why? Join us for a discussion about the human body and its adaptations to a world filled with predators, pathogens and parasites. Bring your appendix, if you still have one, and learn about its special purpose.
About the Speaker:
Rob Dunn is an ecologist in the Department of Biology at North Carolina State University where he studies the global distribution of life and how it is changing as we change the world. He also studies ants. Dunn’s award-winning book “Every Living Thing” (Harper Collins, 2009) explores the strange limits of the living world and the stranger scientists that study them. His next book, “Clean Living is Bad for You … and Other Modern Consequences of Having Evolved in the Wild,” will be out in 2010. Dunn also writes articles for magazines including National Geographic, Natural History, Seed, Scientific American and National Wildlife. To read more of Rob’s writing, sign up for his email list at:
http://groups.google.com/group/Smallthingsconsidered.
RSVP to katey.ahmann@ncmail.net. For more information, contact Katey Ahmann at 919-733-7450, ext. 531.

ScienceOnline2010 session videos – Science and Entertainment Part 4

Science and Entertainment: Beyond Blogging
Saturday, January 16 at 2 – 3:05pm
D. Science and Entertainment: Beyond Blogging – Tamara Krinsky and Jennifer Ouellette
Description: Over the past several years, the Internet has tangibly changed the way that movies and TV shows are produced and marketed. Blogs will call out ridiculous scientific errors found in stories and the critique can go viral very quickly; therefore, science advising is on the rise in an attempt to add some semblance of plausibility to your favorite flicks. As tools on the web continue to evolve, filmmakers and television creators are finding new ways to connect with and market to their viewers. For some shows, this has meant tapping into the science featured in their content, ranging from an exploration of the roots of the science that has been fictionalized to the expansion of a scientific topic explored in a documentary. In this session, we’ll look at how online video and social networking tools are playing a part in connecting science, Hollywood and its fans.

New and Exciting in PLoS ONE

There are 25 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:

Continue reading

Clock Quotes

I’ve just learned about his illness. Let’s hope it’s nothing trivial.
-Irvin S. Cobb

Why it is important for media articles to link to scientific papers

You may be aware that, as of recently, one of my tasks at work is to monitor media coverage of PLoS ONE articles. This is necessary for our own archives and monthly/annual reports, but also so I could highlight some of the best media coverage on the everyONE blog for everyone to see. As PLoS ONE publishes a large number of articles every week, we presume that many of you would appreciate getting your attention drawn to that subset of articles that the media found most interesting.
So, for example, as I missed last week due to my trip to AAAS, I posted a two-week summary of media coverage this Monday. And that took far more time and effort (and some silent cursing) than one would expect. Why?
I don’t think I am a slouch at googling stuff. Some people joke that the entire Internet passes through my brain before it goes to the final audience. After all, I have been monitoring the Web for mentions of ‘PLoS’ and ‘Public Library of Science’ on blogs, Twitter, FriendFeed, Facebook and elsewhere for a few years now. If I don’t catch a mention within minutes of it being posted, you can bet one of my many online friends/followers/subscribers is bound to quickly let me know by e-mail or Direct Messaging somewhere. If someone says something nice about PLoS, I am quick to post a ThankYou note. If someone asks a question, I try to answer or to connect the person with the appropriate member of the PLoS staff. If someone is publicly musing about submitting a manuscript to one of our journals, I am right there to give encouragement. If someone makes a factual error, I gently correct it. It is very, very rare that I need to raise the Immense Online Armies because someone is wrong on the Internet 😉
So, why is it difficult then to compile a collection of weekly media coverage? Let me walk you through the process….
First, as you probably already know, PLoS makes no distinction between Old and New media. We have bloggers on our press list who apply/sign-up in the same way and abide by the same rules as traditional journalists (and, unlike mainstream media, bloggers NEVER break embargos, not once in the past three years since we started adding bloggers to our press list). For the kind of coverage we prefer to see, we point bloggers to the ResearchBlogging.org criteria. In return, bloggers can send trackbacks to our articles, their work is showcased side-by-side with the traditional outlets in our weekly posts, they can be discovered via Google Blogsearch, Postgenomic and ResearchBlogging.org links directly from each article, and one blogger per month wins a t-shirt and special recognition.
So, I start with blog posts first. The first thing I do is take a look at ResearchBlogging.org. Those are the best of the best posts – not merely mentioning our articles, but adding analysis, commentary, critique, context and additional information. How do I find them? I just search the site for the phrase ‘journal.pone‘. That search brings up every single post that mentions a PLoS ONE article because that phrase is a part of every possible form of the URL of the article (including the shortest one, which includes just the DOI). If a post links to our article (and that is the only way to get aggregated on ResearchBlogging.org) I will find it this way. Needless to say, this process takes just a few minutes per week.
Knowing that there are some good blogs out there that are not registered at ResearchBlogging.org (which is strange and unfathomable why – RB.org is a ‘stamp-of-approval’ place for science blogs recognized by the outside world of journals and media, as well as a nice way to get extra recognition and traffic, and even awards), I then repeat the same search – for ‘journal.pone‘ – on Google Blogsearch. This may bring up a few more posts that I did not catch yet. Occasionally, some of these are good. Another couple of minutes. Blogs are now done. Move on to traditional media….
And this is where the Hell starts. Try searching Google News for ‘journal.pone‘…?! All I get are a couple of prominent blogs that I have already counted, e.g., those blogs that are listed by Google News (scienceblogs.com blogs, Ars Technica, Wired blogs, etc.). Where are the others?
The problem is, nobody in the mainstream media links to papers.
So I have to search for PLoS and for Public Library Of Science and then figure out which ones are covering specifically PLoS ONE articles (sometimes they don’t specify, sometimes they name the wrong journal – last week an article on PLoS Current-Influenza was reported to be in PLoS ONE by a number of outlets copying the error from each other). Then I have to search for keywords for individual articles I suspect may have received some coverage. Last week, for example, I searched for “swallows+antioxidants” and “St. Birgitta”, among many others. This lasts for hours! And at the end I am still not 100% sure I caught everything. How frustrating!
Not just is there a big difference in time and effort spent between finding blog posts and finding media articles, but there is an even bigger disparity when one considers what results come out of these searches. I have been doing this for a month now. I expected that there would be poor blog posts and poor media articles, that there would be good blog posts and good media articles, and that there would occasionally be some excellent blog posts and excellent media articles. So far, that is true…. except I have yet to discover an excellent media article. As a rule, the very best coverage of every paper in the past month was done by a blogger or two or three. Then there are some other, good pieces of coverage in both the New and Old media, and then there are some really bad pieces in both realms as well (not all blog posts I count here are really bad – they may just be too detailed, technical and dry for lay audience because the blogger is intentionally targeting scientific peers as audience, which is fair thing to acknowledge).
So, every week, it takes me a few minutes to find the very best coverage (which is on blogs, usually those aggregated on ResearchBlogging.org). And then I spend hours looking for remnants, in the traditional media, which turn out to be so-so, some OK, some not so good, some horrible. If I wasn’t paid to do this, I would not do it – it cannot be good for my long-term mental health.
The resistance to post links is an atavism, a remnant of an old age before the Web. I know (because I asked many times) many good science journalists keep trying to add links, but the editors say No. The traditional media has still not caught on to the Ethic of the Link, which is an essential aspect of ethics of online communication.
I can think, off the top of my head, of three good reasons why everyone who publishes online should include a link to the scientific paper described in the article (just post the DOI link that comes with the press release if you are on the press list – if it does not resolve immediately, it is not your fault, you can always blame the journals for being slow on it – though this should never happen with PLoS articles):
Reason One: I will not go crazy every week. I am assuming that every scientific publisher has people on the staff whose task is to monitor media coverage and each one of these people is cussing and cursing YOU, the Media, every day. Try to make friends with people who provide you with source material on a regular basis.
Reason Two: Media coverage is one of the many elements of article-level metrics. Furthermore, links from the media affect the number of views and downloads of the article, and those are also elements of article-level metrics. Number of views/downloads then, in the future, affects the number of citations the work gets which is also and element of article-level metrics. Thus omitting the link skewes the ability of readers and observers to evaluate the papers properly.
The current ecosystem of science communication has a scientific paper at its core, additions to the paper (e.g., notes, comments and ratings, as well as Supplemental materials, videos posted on Scivee.tv, etc) as a shell, and incoming and outgoing links – trackbacks, cited papers, citing papers, links to other papers in the same Collection, links to other papers with the same keywords, and yes, incoming links from the media – as connections building a network: the entire inter-connected ecosystem of scientific knowledge.
By not linking to scientific papers, traditional media is keeping itself outside of the entire ecosystem of empirical knowledge. By doing this, the traditional media is fast making itself irrelevant.
Reason Three: if an article in the media discusses a scientific study, that scientific paper is the source material for the article. If the link is missing, this is an automatic red flag for the readers. What is the journalist hiding? Why is the article making it difficult for readers to fact-check the journalist? Something does not smell good if the link is not provided (or worse, it is impossible to figure out even who are the authors and in which journal did they publish – yes, that is more common than you think).
The instant and automatic response of the readers is mistrust. Every time you fail to link to the paper, you further erode whatever trust and reputation you still may have with the audience. You soon cease to be a legitimate source of information. Sure, most readers will not go hunting for the paper to read it in order to fact-check you. But two or three will, and they will let everyone else know if your article is trustworthy or not, either in the comments under the article on your own site, or on their blogs which will be quickly picked up by Google (remember: Google loves blogs).
So please, media types, hurry up and catch up with the world. The 21st century is already a decade in – you really need to do some very fast learning. Right now. Or you’ll go extinct in a nanosecond. And despite my reputation, I never said that I’d consider that result to be a Good Thing. We are in this together, you just need to do your part. To begin with, start linking.

New user functionality at PLoS – referenced PDFs via Pubget

Often when a scientific paper gets cited, one wants to see how exactly it was cited. Thus one needs to download the citing article. There are numerous ways to do so, but starting today, you can get this done with just a click or two on all PLoS articles. How?
Go to the Metrics tab of the article, scroll down until you see CrossRef citations, click to expand the list of papers that cite the paper you are on. You will see, next to some papers, a tiny PDF icon. Clicking on that icon will open the PDF of the paper you are looking for.
How is that possible? PLoS partnered with PubGet to make this work. Unfortunately, not every article has the PDF icon because not every paper is freely accessible. It works with Open Access articles, but if the paper is not, then it may still work if you are affiliated with one of the 170 institutions in the PubGet network. If your institution is not a part of their network, you should work on getting it included there: just tell your library – Pubget is free.
But it is hard to explain how cool and quick and easy this is in mere words. It is much better to use the magic of screencast video, so here is a brief tutorial:

Dan Ariely – Behavioral Economics seminar

At North Carolina State University next week:

Seminar: Wednesday, March 10th, 4PM
Dr. Dan Ariely
James B. Duke Professor of Behavioral Economics, Duke University
Who Put the Monkey in the Driver’s Seat?
Venue: Room 101 David Clark Laboratories
The NCSU, W. M. Keck Center for Behavioral Biology is pleased to sponsor a seminar by a scholar in the field of Behavioral Economics who is also recognized for his ability to communicate the fascinating findings in this field to the public. When we make “decisions” we think that we are in control. Dan Ariely explains some of the hidden forces that actually control those decisions.
See:
http://topics.npr.org/topic/Dan_Ariely/articles
http://www.ted.com/speakers/dan_ariely.html

Blog posts about Open Laboratory 2009 so far

Neurophilosophy
Code of Life
The Culture of Chemistry
Neurotopia
NeuroDojo
The Loom
Urban Science Adventures
Aardvarchaeology
Archy
The Flying Trilobite
Rigor Vitae
Bench TwentyOne
Page 3.14
The Scientific Activist
Science After Sunclipse
Mr Science Show
Byte Size Biology
Neurotopia
A Blog Around The Clock

ScienceOnline2010 – interview with Andrew Thaler

Continuing with the tradition from last two years, I will occasionally post interviews with some of the participants of the ScienceOnline2010 conference that was held in the Research Triangle Park, NC back in January. See all the interviews in this series here. You can check out previous years’ interviews as well: 2008 and 2009.
Today, I asked Andrew Thaler from Southern Fried Science to answer a few questions.
Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your (scientific) background?
thaler-headshot.jpgI’m originally from Baltimore, but moved to North Carolina 8 years ago for undergrad and never looked back. I currently live in Beaufort, NC. I’m working towards my Ph.D in Deep Sea Population Genetics at the Duke University Marine Lab. I was the kid who wanted to be a marine biologist since I was six.
Philosophically I guess you could call me a Happy Fatalist. We’ve profoundly changed the world and anthropogenic influences on the environment are going to be the driving force for almost all societal change in the foreseeable future, but I’m less panicked about the way things are changing and more excited to be part of the largest experiment in human history. Most of the changes we’re going to see in the next few decades are unavoidable, we’ve passed the tipping point. People are often afraid to admit that, but eventually we need to not just reduce our impact on the environment, but also preparing for the major changes that are going to happen. We love to promote the myth of a balanced environment that’s somehow being upset, but the environment is always changing. The sooner we accept that environmentalism is about human values and not so archetypal perfect environment, the better off we’re going to be in the long run.
So I come from the position that we need to shift our focus from how to prevent changes to how we’re going to deal with the inevitable.
My scientific background is largely in marine biology and population genetics, with a brief segue into mycology for a couple of years.
Tell us a little more about your career trajectory so far: interesting projects past and present?
I started off working as an Aquarist Assistant at the National Aquarium in Baltimore rearing seahorses. That was my first real chance to design my own experiments. I was part of the Syngnathid Breeding Program, and some of my seahorses are still swimming around aquariums throughout the world. From there I upgraded to a lab tech in a Mycology lab before entering grad school. I started my grad career studying the biodiversity of deep sea fungi that occur at methane seeps. No one had ever really looked at deep sea fungi, so I thought I was all cool breaking new ground. As it turns out, there just isn’t that much fungi down there, or if there is, it’s very elusive. I’m currently putting together a crowdsourced guide to conservation genetics geared towards managers and the general public.
What is taking up the most of your time and passion these days? What are your goals?
Right now I’m just trying to make it through my Preliminary exams intact. Blogging is acting as my stress relief outlet (which is why most of my posts recently have been jokes about Global Draining). Other than that, I’m brewing experimental beers. My last batch I replaced all of the grains with green tea leaves to create a sort of Green Tea Pale Ale. It should be ready in a couple weeks, so I’ll let you know how it turns out.
What aspect of science communication and/or particular use of the Web in science interests you the most?
I’ve been really excited about Twitter lately. Suddenly I have a huge collection of experts available whenever I need them. Just send out a quick question and I usually get 5 or 6 answers by the end of the day.
How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, FriendFeed and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?
My undergrad institution was one of the first to get Facebook, so I’ve been on it for pretty much my entire academic career, so I have no idea if it’s been a net positive or negative. Twitter for sure is neutral, I get tons of help from my twitter network, but it can also be a huge time sink. All in all I feel like online activity follows the old (ways to be more efficient)/(ways to procrastinate) = no net change.
When and how did you first discover science blogs? What are some of your favourites? Have you discovered any cool science blogs by the participants at the Conference?
I got into science blogging through Kevin Zelnio, who I share an office with. My favorites are for sure the marine blogs – Deep Sea News, Oyster’s Garter (which I guess is Deep Sea News now too), Malaria, Bedbugs, Sea Lice, and Sunsets, blogfish. I met nearly all the cool science blogs I follow from Science Online 09 and this years conference.
What was the best aspect of ScienceOnline2010 for you? Any suggestions for next year? Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?
This was the first time I went in with a smart phone, and the amount of content that was streaming out of the twitterverse was astounding. It was almost like I could listen in on four conferences at once. It might be nice to have a closing keynote to bring everyone back together at the end of the meeting as well as the beginning.
It was so nice to see you again and thank you for the interview. I hope to see you again next January.
Thank you and I can’t wait for the next conference.

Nanomaterials in Ecosystems: Should we worry?

Duke’s Periodic Tables at the Broad Street Cafe
March 9, 2010 | 7:00 P.M.
Nanomaterials in Ecosystems: Should we worry?
Nanotechnology has the enormous potential to change our society. New advances in medicine, energy production, environmental cleanup and better access to clean water are just a few of the many possibilities. According to the Project on Emerging Nanotechnologies, the number of products that use nanomaterials has increased almost 380% since 2006. But, is it the same special properties that make nanoscale materials so useful that also pose potential risks to humans and the environment? Join Dr. Emily Bernhardt from the Center for the Environmental Implications of NanoTechnology to discuss the fate of nanomaterials in our environment and why you should care.
Speaker: Dr. Emily Bernhardt, Assistant Professor of Biology at Duke University and Program Leader at the Center for Environmental Implication of NanoTechnology

ScienceOnline2010 session videos – Science and Entertainment Part 3

Science and Entertainment: Beyond Blogging
Saturday, January 16 at 2 – 3:05pm
D. Science and Entertainment: Beyond Blogging – Tamara Krinsky and Jennifer Ouellette
Description: Over the past several years, the Internet has tangibly changed the way that movies and TV shows are produced and marketed. Blogs will call out ridiculous scientific errors found in stories and the critique can go viral very quickly; therefore, science advising is on the rise in an attempt to add some semblance of plausibility to your favorite flicks. As tools on the web continue to evolve, filmmakers and television creators are finding new ways to connect with and market to their viewers. For some shows, this has meant tapping into the science featured in their content, ranging from an exploration of the roots of the science that has been fictionalized to the expansion of a scientific topic explored in a documentary. In this session, we’ll look at how online video and social networking tools are playing a part in connecting science, Hollywood and its fans.

Today’s carnivals

Scientia Pro Publica #22 is up on Reciprocal Space
Carnival of Evolution #21: The Superstar Edition is up on Mauka to Makai
Festival of the Trees #45 is up on The Voltage Gate
Grand Rounds Volume 6 number 23 are up on Doctor Anonymous

New and Exciting in PLoS this week

Four of the seven PLoS journals post new articles on Monday nights – let’s see what is exciting and bloggable 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:
Predation upon Hatchling Dinosaurs by a New Snake from the Late Cretaceous of India:

Snakes first appear in the fossil record towards the end of the dinosaur era, approximately 98 million years ago. Snake fossils from that time are fragmentary, usually consisting of parts of the backbone. Relatively complete snake fossils preserving skulls and occasionally hindlimbs are quite rare and have only been found in marine sediments in Afro-Arabia and Europe or in terrestrial sediments in South America. Early snake phylogeny remains controversial, in part because of the paucity of early fossils. We describe a new 3.5-m-long snake from the Late Cretaceous of western India that is preserved in an extraordinary setting–within a sauropod dinosaur nest, coiled around an egg and adjacent the remains of a ca. 0.5-m-long hatchling. Other snake-egg associations at the same site suggest that the new snake frequented nesting grounds and preyed on hatchling sauropods. We named this new snake Sanajeh indicus because of its provenance and its somewhat limited oral gape. Sanajeh broadens the geographical distribution of early snakes and helps resolve their phylogenetic affinities. We conclude that large body size and jaw mobility afforded some early snakes a greater diversity of prey items than previously suspected.

This paper was already blogged by Anne-Marie Hodge and Ed Yong. Also read the associated primer: Studying Function and Behavior in the Fossil Record:

Inferring the behavior and function of ancient organisms is hard. Some paleontologists would say that it cannot be done because such hypotheses can never be testable, whereas others would say that this is surely a prime task for paleontology–to seek to bring ancient organisms back to life.
These issues have long troubled paleontologists. The founder of comparative anatomy, Georges Cuvier (1769-1832), insisted on the common pattern of the skeleton of living and fossil vertebrates and that anatomy could be reconstructed with confidence from incomplete fossil remains. Further, he argued that the skeleton of a living or extinct animal held unequivocal clues about function and behavior. Cuvier saw his mission to establish rules for comparative anatomy that would allow paleontologists to make certain statement with clarity and confidence [1], a key principle today, what one might call “evidence-based reconstruction” (for example, sharp teeth indicate a diet of meat rather than plants, or mammalian characters in the teeth indicate that the unknown animal was endothermic and nourished its young from mammary glands) as opposed to speculation (“this dinosaur was purple because I guess it was”).

Canine Morphology: Hunting for Genes and Tracking Mutations:

As a result of domestication, selection for desirable phenotypes, and breed propagation, the domestic dog is unmatched in its diversity as a land mammal. Exhibiting extraordinary levels of both interbreed heterogeneity and intrabreed homogeneity, evidenced in part by the extensive linkage disequilibrium observed in many breeds, the dog provides an as-yet unrealized opportunity to uncover the molecular mechanisms that govern natural variation across mammalian species. We herein discuss recent advances in canine genomics that have made exploration of genetic mechanisms controlling breed-specific differences possible. We consider some examples where molecular mechanisms controlling simple traits have been uncovered. Finally, we reveal how combinations of genes produce complex phenotypes that can be revealed through studies of dog breeds featuring specific traits.

Atlantic Cod Piscidin and Its Diversification through Positive Selection:

Piscidins constitute a family of cationic antimicrobial peptides that are thought to play an important role in the innate immune response of teleosts. On the one hand they show a remarkable diversity, which indicates that they are shaped by positive selection, but on the other hand they are ancient and have specific targets, suggesting that they are constrained by purifying selection. Until now piscidins had only been found in fish species from the superorder Acanthopterygii but we have recently identified a piscidin gene in Atlantic cod (Gadus morhua), thus showing that these antimicrobial peptides are not restricted to evolutionarily modern teleosts. Nucleotide diversity was much higher in the regions of the piscidin gene that code for the mature peptide and its pro domain than in the signal peptide. Maximum likelihood analyses with different evolution models revealed that the piscidin gene is under positive selection. Charge or hydrophobicity-changing amino acid substitutions observed in positively selected sites within the mature peptide influence its amphipathic structure and can have a marked effect on its function. This diversification might be associated with adaptation to new habitats or rapidly evolving pathogens.

Modeling Disease Vector Occurrence when Detection Is Imperfect: Infestation of Amazonian Palm Trees by Triatomine Bugs at Three Spatial Scales:

Blood-sucking bugs of the genus Rhodnius are major vectors of Chagas disease. Control and surveillance of Chagas disease transmission critically depend on ascertaining whether households and nearby ecotopes (such as palm trees) are infested by these vectors. However, no bug detection technique works perfectly. Because more sensitive methods are more costly, vector searches face a trade-off between technical prowess and sample size. We compromise by using relatively inexpensive sampling techniques that can be applied multiple times to a large number of palms. With these replicated results, we estimate the probability of failing to detect bugs in a palm that is actually infested. We incorporate this information into our analyses to derive an unbiased estimate of palm infestation, and find it to be about 50% – twice the observed proportion of infested palms. We are then able to model the effects of regional, landscape, and local environmental variables on palm infestation. Individual palm attributes contribute overwhelmingly more than landscape or regional covariates to explaining infestation, suggesting that palm tree management can help mitigate risk locally. Our results illustrate how explicitly accounting for vector, pathogen, or host detection failures can substantially improve epidemiological parameter estimation when perfect detection techniques are unavailable.

Clock Quotes

The writer who possesses the creative gift owns something of which he is not always master – something that at time strangely wills and works for itself.
– Charlotte Bronte

Science of airport security screening

At Morehead Planetarium in Chapel Hill this week:

SCIENCE & ETHICS: AIRPORT SECURITY
Thursday, March 4, 7 p.m.
Michael Zunk,
Federal Security Director, TSA, RDU International Airport
Come hear Mr. Zunk discuss scanning technologies while busting some popular myths on airport security screening.
Cookies and coffee served.

Morehead Banquet Hall, East Entrance, 2nd Floor. Chapel Hill, NC.

ScienceOnline2010 – interview with Andrea Novicki

Continuing with the tradition from last two years, I will occasionally post interviews with some of the participants of the ScienceOnline2010 conference that was held in the Research Triangle Park, NC back in January. See all the interviews in this series here. You can check out previous years’ interviews as well: 2008 and 2009.
Today, I asked Andrea Novicki from the Duke CIT blog to answer a few questions.
Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your (scientific) background?
Andrea Nowicki pic.JPGHi, thank you so much for asking. I’m currently employed at Duke University in the Center for Instructional Technology as an academic technology consultant for the sciences – I work with faculty who teach science or math, to help them figure out how to effectively and efficiently help students learn, using technology. My work is a satisfying combination of science, education and technology. Scientifically, I began as a marine biologist as an undergraduate and in early grad school; still, marine biology feels like my natural home. I became inspired by a summer course to study neural systems and behavior, because investigating changes in behavior at the level of changes in molecules in single, identified neurons was both exciting and satisfying. After a couple of postdocs and a tenure track faculty position, I stepped away from research and teaching and I went sailing, driven by a restless sense of adventure. I’m now back in academia, working with smart, interesting people.
Tell us a little more about your career trajectory so far: interesting projects past and present?
I have been involved with some great projects; if there is a theme, it is change, both in my research projects and in my career. I’ve investigated the neural pathways that mediate color change in squid and octopus and I participated in research cruises identifying midwater ocean animals. On land I worked with insects, monitoring and altering activity in single neurons that correlate with behavior change, and predicting and then, satisfyingly, finding a neuron with particular characteristics.
I (and many other people) began to question the traditional lecture way that science was taught and early on, I began using computers and technology to help students learn biology.
What is taking up the most of your time and passion these days? What are your goals?
My goals? Do I have to be realistic? I’d like to contribute to making science accessible; I’d like for everyone to recognize the beautiful complexity and interconnectedness of the natural world at all scales, and find joy of figuring out for themselves how things work.
What aspect of science communication and/or particular use of the Web in science interests you the most?
I’m excited about the increased openness and social nature of science. In my grad school days, the model was that successful scientists kept to themselves until they published, and then only in reputable, peer-reviewed journals; anything else was considered frivolous and distracting. Now, because of the web, science is now more public and more accessible (accessible both technologically and in presentation style). I’m a huge fan of Jean-Claude Bradley’s open notebook science approach, ever since I heard him speak at the first science blogging conference. This project (and many others) make the process of science more open. Passionate blogs by students and post docs as well as people who run their own labs show what science is really like – it’s done by caring people with feelings and emotions, not just some distant, always-right white-coated professor. This openness about the process, as well as the explanations of results made accessible (like at researchblogging.org) have the potential to illustrate the appeal of science to everyone.
I’d like to see people use some of the new visualization tools to explore publically available data sets to make new discoveries, just because they are curious, regardless of their final degrees or institutional affiliation.
How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, FriendFeed and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?
I lurk on numerous blogs, and I love scienceblogs, it’s a great way to keep up on how science is changing, and visit my favorite topics. I’m very fortunate, in that monitoring how people use technology to communicate science (for science education) is part of my job. I follow people on Twitter and find it a useful way to find new ideas and resources, and contribute occasionally. Although I do have an account on Facebook, I rarely look at it.
I do contribute to a blog, but it’s more about technology in education than about science, and is part of my job. As a confirmed introvert, I find blogging difficult. I am, by nature, a lurker. I’m in awe of people who can toss off a post without thinking it over and over and over.
In other words, all of this online activity is necessary for my work; I do not contribute enough, but I benefit tremendously.
What was the best aspect of ScienceOnline2010 for you? Any suggestions for next year? Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?
Every session I attended was thought-provoking! Stacy Baker’s students stole the show again; my notes have many observations about their attitudes towards technology. I also welcomed the sessions by librarians – their ability to find information, and think about how it is organized will continue to be invaluable.
I observed that the conference had many people attending who were not exactly science bloggers (people like me, for example), which showed how many options there are for people to participate in science online in some way, even if they are not, strictly speaking, science bloggers.
There’s still something wonderful about meeting someone for the first time after you’ve already read their writing – it’s like you can peek into their brain. When you meet a blogger (or any writer), your first impression has already been formed and modified and added to, and their physical appearance is irrelevant. It’s an almost utopian ideal – people are judged by the quality of their thoughts, not what they look like.
At one session, during a discussion of Google Earth and GIS, Cameron Neylon thought aloud about using visualizations as a way of distributing data, which is something I had been thinking about, as a way of making science, and raw data, more accessible. He, of course, said it more elegantly and I will be thinking about this for some time. How can good visualizations be used as a way of distributing data, in a way that does not immediately shape a conclusion but allows for exploration?
It was so nice to see you again and thank you for the interview. I’m sure I’ll see you before then, and I expect you’ll join our event again next January.

How to organize an Interactive Conference

On Friday, I was on Skeptically Speaking radio show together with Reed Esau (who organized the Skepticamp) talking about ScienceOnline2010, what it takes to organize it, the Unconference format and why it is good, etc.
You can now listen to the recording of the show here.

ScienceOnline2010 session videos – Science and Entertainment Part 2

Science and Entertainment: Beyond Blogging
Saturday, January 16 at 2 – 3:05pm
D. Science and Entertainment: Beyond Blogging – Tamara Krinsky and Jennifer Ouellette
Description: Over the past several years, the Internet has tangibly changed the way that movies and TV shows are produced and marketed. Blogs will call out ridiculous scientific errors found in stories and the critique can go viral very quickly; therefore, science advising is on the rise in an attempt to add some semblance of plausibility to your favorite flicks. As tools on the web continue to evolve, filmmakers and television creators are finding new ways to connect with and market to their viewers. For some shows, this has meant tapping into the science featured in their content, ranging from an exploration of the roots of the science that has been fictionalized to the expansion of a scientific topic explored in a documentary. In this session, we’ll look at how online video and social networking tools are playing a part in connecting science, Hollywood and its fans.

The Best of February

I posted 126 times in February.
The Biggest Event of the month, of course, was the release of The Open Laboratory 2009, the fourth annual anthology of best writing on science blogs. And the first book review came out shortly after.
The Second Biggest Event of the month? It involves Science! I published a paper and blogged all about it – My latest scientific paper: Extended Laying Interval of Ultimate Eggs of the Eastern Bluebird.
Third Best Post of the month? I can’t have a month pass by without writing something provocative – Why is ‘scientists are bad communicators’ trope wrong.
There was an interesting excercise going on Twitter recently, and I donned my rhetoricians’s hat for Using Twitter to learn economy of words – try to summarize your research paper in 140 characters or less!
Early in February, there were several interesting Science Blogging News including the ResearchBlogging.org Awards. Later, the finalists were announced. Winners? Next month.
I went to the AAAS meeting in San Diego, but did not blog much from there, because there was no wifi and I was not regarded as press. My co-panelist Dennis Meredith did a fun presentation, which is available online. Our session had a lot of coverage, which I collected here. A few other Sciblings went to AAAS and I compiled their blog posts (with some commentary) here.
Following ScienceOnline2010, I started interviewing some of the participants. In February, I posted Q&As with Ken Liu, Maria Droujkova, Hope Leman, Tara Richerson, Carl Zimmer, Marie-Claire Shanahan, John Timmer, Dorothea Salo, Jeff Ives and Fabiana Kubke. Since there was so much conference blogging about the state of science journalism, I collected all the links about the topic in one place. And almost every day I posted one of the videos from the sessions and events at ScienceOnline2010 as well.
Some North Carolina science journalism/blogging projects I am involved with are getting noticed by the outside world, so I had to blog about it.
I wrote two posts highlighting some of the youngest science bloggers out there and asked readers to post comments on their blogs. Then I had to add a similar third post as more such student bloggers surfaced and needed ecnouragement in their blogs’ comment sections.
I went to see the new shark exhibit and a shark talk at the NC Museum of Natural Science and wrote about them: Megalodon and other sharks at Darwin Day.
Cool site of the week? I introduced Aves 3D.
Work-related, PLoS Store unveiled its Spring Collection: T.rex, Space, lively colors, mugs, and future scientists – the PLoS Store Spring Collection. As always on the 1st of the month, I announced January 2010 PLoS ONE Blog Pick Of The Month

New and Exciting in PLoS ONE

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:

Continue reading

Clock Quotes

He is a self-made man and worships his creator.
– John Bright

PLoS ONE Blog Pick of the Month for February 2010….

…goes to….you’ll need to click here to see.

Today’s carnivals

Circus of the Spineless #48: Cabinet of Curiosity is up on Matthew Sarver: The Modern Naturalist
Diversity in Science Carnival #7: Black History Month – Broadening STEM Participation at every level – is up on Urban Science Adventures! ©
Carnival of the Green #215! is up on Project Earth
The 131st Skeptics’ Circle is up on Providentia
Friday Ark #284 is up on Modulator

The first review of Open Laboratory 2009

OpenLab09The fourth anthology barely managed to hit the virtual shelves when the very first book review was published. Of course, considering the speed, this was done by a blogger – Grant Jacobs from the ‘Code for Life’ blog on New Zealand sciblogs. Read his review here.
You liked what you just read? Buy the book!
And if that is not enough for you, check out the 2006, 2007 and 2008 editions. Or buy a few now and save them for presents for next Christmas….

ScienceOnline2010 session videos – Science and Entertainment Part 1

Science and Entertainment: Beyond Blogging
Saturday, January 16 at 2 – 3:05pm
D. Science and Entertainment: Beyond Blogging – Tamara Krinsky and Jennifer Ouellette
Description: Over the past several years, the Internet has tangibly changed the way that movies and TV shows are produced and marketed. Blogs will call out ridiculous scientific errors found in stories and the critique can go viral very quickly; therefore, science advising is on the rise in an attempt to add some semblance of plausibility to your favorite flicks. As tools on the web continue to evolve, filmmakers and television creators are finding new ways to connect with and market to their viewers. For some shows, this has meant tapping into the science featured in their content, ranging from an exploration of the roots of the science that has been fictionalized to the expansion of a scientific topic explored in a documentary. In this session, we’ll look at how online video and social networking tools are playing a part in connecting science, Hollywood and its fans.

Clock Quotes

Something of vengeance I had tasted for the first time; as aromatic wine it seemed, on swallowing warm and racy; its afterflavor, metallic and corroding, gave me a sensation as it I had been poisoned.
– Charlotte Bronte

Using Twitter to learn economy of words – try to summarize your research paper in 140 characters or less!

A couple of weeks ago, there was a flurry of tweets, tagged with #sci140 hashtag on Twitter. What was that about? People were trying to summarize scientific papers in 140 characters or less. Actually, they had to use less as the hashtag itself took some space.
Almost 200 tweets were made, and they have all been collected (and the winners chosen) in this blog post on f1000 blog.
I found the exercise fascinating!
First, it was quite incredible how many more people chose to tweet well-known classical papers compared to those tweeting their own (thus obscure) publications. I would not call it cheating, but summarizing stuff that’s in textbooks is much easier. Why?
First, you don’t need to spend another several characters in order to include a link – a must if one tweeted their own paper. Why link to Pasteur, Darwin, Shroedinger, Newton, Galileo, Watson&Crick or Pavlov when everyone already knows what they did? I had to link to my papers when I tweeted them – a tweet was like a press title: not a joke, not a definitive description, but a bait for the reader to get sufficiently curious to click on the link and read the paper itself.
Second, there is so much that one could assume readers already knew about the well-known historical papers (and sometimes entire books!). Tweeting a Classic was more an exercise in witty hinting as to which paper was mentioned than actually explaining it – those who tweeted their own papers had no such luxury: they had to really summarize the papers.
Then, looking at only the tweets summarizing people’s own publications, thus obscure publications that could not be just hinted about, it could be seen that they had two distinct flavors. Some people decided to use the space to say what they did (methods) and others decided to say what they discovered (conclusions). Nobody said why the study was relevant or important to lay audience on Twitter. Obviously, the character limit makes it impossible to include all three. Why did people make choices they did? Who chose methods, who chose conclusions, and why?
I found tweets about people’s own papers fascinating. Why are these tweets so much clearer about the papers than the actual official titles of those same papers? Can we or should we try to make our papers’ titles so short yet so informative as if they will be tweeted in full?
Twitter forces one to think about the economy of words, to become much more efficient with one’s use of language. It takes work and thought and practice to get to the point of tweeting truly well. I remember Jay Rosen once saying that some of his tweets take 45 minutes to compose and edit until he is satisfied that the text uses the words for maximal clarity and impact. There is no luxury in using superfluous language and the result can be a crystal-clear statement or description that far outshines the often-wordy original.
Go look at the collected tweets. What do you think?
Then, I want to issue a challenge. All these tweets were done by working research scientists. I would like to see how professional science journalists, writers and editors would tweet those same exact papers, using the same #sci140 hashtag.
Are professional users of economic language better or worse than people who deeply understand the underlying science but were never trained to be economical with language? Go try….

SciBlings at AAAS10

Four Sciblings (and three ex-Sciblings – Sheril Kirshenbaum, Chris Mooney and Carl Zimmer – but once a Scibling always a Scibling rule applies, so we hung together some…) went to the AAAS meeting last week in San Diego. There is a lot of coverage in the MSM (and a little bit on blogs – it’s hard to blog when you are not given tools, access and respect and thus AAAS will get much less, and much less positive coverage than they would have otherwise) – but here I just want to link to what my SciBlings have posted so far (I will post some more myself later – just watch the AAAS10 category here):
Jennifer Jacquet: Do Scientists Want to Bridge Science and Society?

So much of what the scientists do is less relevant than it could be. This was the motivation behind the theme at the 2010 AAAS annual meeting, Bridging Science and Society….

Josh Rosenau: Highlights from TIMSS 2007 at AAAS:

A message in lots of the science communication and science policy sessions has been that scientists and senior science educators need to be better communicators. Learning what works and what doesn’t should be of interest to all of them, so I have to agree it’s a shame to see the room so empty.

Josh Rosenau: Called out:

The organizer of this education session caught me blogging her remarks, but I didn’t get sent to sit in the corner.

Josh Rosenau: Lubchenco:

Who has two thumbs and met NOAA administrator, jetsetting ecologist, and hero to policy-loving scientists Jane Lubchenco?

Oh, btw, I got to briefly talk to Jane Lubchenco as well.
Josh Rosenau: AAAS Day 3: Social media in science:

The existence of quacks on blogs doesn’t invalidate the enterprise of good bloggers, any more than Fox News invalidates TV journalism or the Washington Times invalidates the New York Times. In any media, you choose your sources based on their expertise and their track record.

Matt Nisbet: Remarks at AAAS Conference on Climate Change Literacy:

There are plans to make available online the various presentation materials, so I will post again when those are ready. In the meantime, I have pasted below the text from remarks I gave as part of a panel on framing.

It is unfortunate that Matt’s session was a part of a pre-conference of which I was not aware until a couple of days before the conference started when I already had the tickets and hotel set. Thus I could not go early to attend his session. It is also unfortunate that he did not stay for the proper AAAS meeting – he left town before I arrived – so he could come to my session. Thus, there could have been two opportunities for Matt and myself to discuss these issues in public, in front of the media, scientists, policy-makers and bloggers. From a couple of e-mails we exchanged, I think that Matt also felt it unfortunate we could not cross swords in public there.
Matt is pretty despised around these quarters (i.e., science blogs in general). The thing is, most of his premises are correct. He just draws wrong conclusions from the premises and thus wrong prescriptions from conclusions (and many, many bloggers have explained, a long time ago and in excruciating detail, where he is right and where he is wrong).
But people who see how obviously wrong his conclusions and prescriptions are, tend to also think that the premises are wrong – and that is just as dangerous as Matt is dangerous when the academic community takes his conclusions and prescriptions seriously. When the 18th century mindset hears mid-20th century ideas, they seem excitingly new – how are they to know that mid-20th century ideas are misguided and already outdated?
I wish we could have used this very visible venue to discuss these issues. Very civilly and politely of course (which has nothing to do with anonymity, as you all know). But, sometimes discourse that seems very civil on the surface, can be devastating. I wish I could have had a chance to employ it. That would have been good for the cause of science communication and the scientific community at large,

Clock Quotes

“I feel so miserable without you, it’s almost like having you here.”
– Comedian Kip Adota

Explaining Science to the Public

Chris Brodie is teaching the ‘Explaining Science to the Public’ class at NC State University. His students come from English, science and engineering departments and he is teaching them how to write well and how to utilize all of the modern technologies for science communication.
The students are now all on Twitter – yup, that’s a class assignment – and you can follow their discussions if you search for the #esttp hashtag.
I visited their class last month and discussed various new forms of online science communication with them. Almost all of them also came to hear a wonderful presentation by Dr.Rick Bonney of Cornell Ornithology Lab about citizen science the other night at Sigma Xi.
Now they have started a class blog – Explaining Science to the Public – and posted their first stories. Chris and students would really appreciate it if you would read and comment on their stories and help them improve their brand-new craft – for most of the students, this is their very first attempt at doing something like this: writing about science for lay audience AND doing it out in public on a blog (so be gentle – these are not seasoned science bloggers, hardened by years of fighting various denialists, pseudoscientists and creationists online in bitter and nasty battles).

How the Hidden Brain Controls Our Lives – new PRI The World Science Forum

Listen to the podcast, post comments, ask questions – the new forum is now live and will go on for the next week:

How the Hidden Brain Controls Our Lives
We like to think of ourselves as conscious, rational beings.
But human behavior is largely driven by unconscious attitudes.
These attitudes reside in the deep recesses of the brain, and we ignore them at our own peril.
So says Washington Post journalist Shankar Vedantam.
Vedantam is the author of a new book, The Hidden Brain: How Our Unconscious Minds Elect Presidents, Control Markets, Wage Wars, and Save Our Lives.
Vedantam explores how the workings of the unconscious mind explain everything from genocide and injustice to the rise of suicide bombers.
The World’s science reporter Rhitu Chatterjee spoke with Vedantam about the role of the hidden brain in our lives and actions. Listen to that interview here.
Download MP3
Now it’s your turn to ask the questions. Join the conversation. It’s just to the right.
* Have you ever regretted a decision you made, realizing later that it was impulsive and ill-informed?
* Do you think it’s possible to change our unconscious biases by better understanding our hidden brains?
* Or does understanding our hidden brains makes us more confused, less sure of our decisions?

ScienceOnline2010 – Journalists: What Scientists to Trust? (video) Part 5

How does a journalist figure out ‘which scientists to trust’?
Saturday, January 16 at 3:15 – 4:20pm
D. How does a journalist figure out “which scientists to trust”? – Christine Ottery and Connie St Louis
Description: We will talk about how science journalists can know which scientists to trust based on a blogpost by Christine Ottery that made a splash in the world of science communication. As a relative newcomer to science journalism and blogging (Christine) and an award-winning broadcaster, journalist, writer and scientist (Connie), we will be bringing two very different viewpoints to the discussion. We will be touching on peer review, journals, reputation and maverick scientists. We will also examine how journalists and scientists can foster good working relationships with each other, find out what is best practice when it comes to sources for science journalists, and turn the premise of the talk on its head and ask “Which journalists can you trust?” of the scientists.

New and Exciting in PLoS this week

Friday is the day when four of our journals publish new articles. Let’s take a look at those I find most interesting (and ‘bloggable’). 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:
Interspecific Hybridization as a Tool to Understand Vocal Divergence: The Example of Crowing in Quail (Genus Coturnix):

Understanding the mechanisms that lead organisms to be separated into distinct species remains a challenge in evolutionary biology. Interspecific hybridization, which results from incomplete reproductive isolation, is a useful tool to investigate such mechanisms. In birds, interspecific hybridization is relatively frequent, despite the fact that closed species exhibit morphological and behavioural differences. Evolution of behaviour is difficult to investigate on a large timescale since it does not ‘fossilize’. Here I propose that calls of hybrid non-songbirds that develop without the influence of learning may help in understanding the gradual process that leads to vocal divergence during speciation. I recorded crows produced by the European quail (Coturnix c. coturnix), the domestic Japanese quail (Coturnix c. japonica) and their hybrids (F1, F2 and backcrosses). Most crowing patterns were intermediate to those of the parental species; some were similar to one or the other parental species, or not present in either parental species. I also observed vocal changes in hybrid crows during the breeding season and from one year to the other. This vocal variability resembles those observed during the ontogeny of the crow in quails. It is likely that similar mechanisms involved in vocal changes during ontogeny might have driven vocal divergence in the species of Palearctic quails. I suggest that hybrid crows might have resembled those produced by intermediary forms of quails during speciation.

Differential Associations of Early- and Late-Night Sleep with Functional Brain States Promoting Insight to Abstract Task Regularity:

Solving a task with insight has been associated with occipital and right-hemisphere activations. The present study tested the hypothesis if sleep-related alterations in functional activation states modulate the probability of insight into a hidden abstract regularity of a task. State-dependent functional activation was measured by beta and alpha electroencephalographic (EEG) activity and spatial synchronization. Task-dependent functional activation was assessed by slow cortical potentials (SPs). EEG parameters during the performance of the Number Reduction Task (NRT) were compared between before sleep and after sleep sessions. In two different groups, the relevant sleep occurred either in the first or in the second half of the night, dominated by slow wave sleep (SWS) or by rapid eye movement (REM) sleep. Changes in EEG parameters only occurred in the early-night group, not in the late-night group and indicated occipital and right-hemisphere functional alterations. These changes were associated with off-line consolidation of implicit task representations and with the amount of SWS but they did not predict subsequent insight. The gain of insight was, however, independently associated with changes of spectral beta and alpha measures only in those subjects from the two sleep groups who would subsequently comprehend the hidden regularity of the task. Insight-related enhancement of right frontal asymmetry after sleep did not depend on sleep stages. It is concluded that off-line restructuring of implicit information during sleep is accompanied by alterations of functional activation states after sleep. This mechanism is promoted by SWS but not by REM sleep and may contribute to attaining insight after sleep. Original neurophysiologic evidence is provided for alterations of the functional activation brain states after sleep. These alterations are associated with a decrease in controlled processing within the visual system and with an increase in the functional connectivity of the right hemisphere, and are supported by SWS in the first half of the night.

Ten Simple Rules for Organizing a Virtual Conference–Anywhere:

Unlike conventional conferences, virtual conferencing permits the involvement of a greater number of participants who would otherwise be unable to participate in events of this breadth owing to (1) limited travel fellowships, if any; (2) lack of time to travel to distant conference locations; and (3) insufficient accommodation and subsistence funds. These factors apply in general to the post-/undergraduate student community and especially to the target audiences that reside in developing countries. Minimizing the requirement to travel also means that the availability of invited speakers is greatly increased, improving the chances of attracting highly relevant and high-impact presenters.
Through the use of video conferencing software, virtual conferences are able to provide an accessible and cost-effective alternative to real time conferences while retaining the key benefits presented by an on-site conference, such as learning opportunities, sharing of ideas, and networking. The use of inexpensive “commodity off-the-shelf” (COTS) technologies permit anyone with an Internet connection, Web cam, and headset to give and/or attend a presentation. According to Andrew Sage, Cisco Systems’ vice president for marketing, virtual conferences “can live on long after the physical booths have been torn down,” while content continues to be viewed in a dedicated virtual environment by many people, even after the conclusion of the event [5].

A Primer on Metagenomics:

Metagenomics is a discipline that enables the genomic study of uncultured microorganisms. Faster, cheaper sequencing technologies and the ability to sequence uncultured microbes sampled directly from their habitats are expanding and transforming our view of the microbial world. Distilling meaningful information from the millions of new genomic sequences presents a serious challenge to bioinformaticians. In cultured microbes, the genomic data come from a single clone, making sequence assembly and annotation tractable. In metagenomics, the data come from heterogeneous microbial communities, sometimes containing more than 10,000 species, with the sequence data being noisy and partial. From sampling, to assembly, to gene calling and function prediction, bioinformatics faces new demands in interpreting voluminous, noisy, and often partial sequence data. Although metagenomics is a relative newcomer to science, the past few years have seen an explosion in computational methods applied to metagenomic-based research. It is therefore not within the scope of this article to provide an exhaustive review. Rather, we provide here a concise yet comprehensive introduction to the current computational requirements presented by metagenomics, and review the recent progress made. We also note whether there is software that implements any of the methods presented here, and briefly review its utility. Nevertheless, it would be useful if readers of this article would avail themselves of the comment section provided by this journal, and relate their own experiences. Finally, the last section of this article provides a few representative studies illustrating different facets of recent scientific discoveries made using metagenomics.

Five Questions about Viruses and MicroRNAs:

MicroRNAs (miRNAs) are ~22-nt regulatory RNAs expressed by all multicellular eukaryotes [1]. Humans encode >700 miRNAs and similar numbers are likely to exist in other mammalian species. Almost all cellular miRNAs are initially transcribed by RNA polymerase II (Pol II) as part of a long, capped, polyadenylated primary miRNA (pri-miRNA) precursor. The miRNA forms part of one arm of an RNA stem-loop that consists of an ~32-bp imperfect stem flanked by unstructured RNA sequences. This stem-loop is recognized by the nuclear RNase III enzyme Drosha, which cleaves the stem to liberate an ~60-nt pre-miRNA hairpin. The pre-miRNA is then transported to the cytoplasm where it is cleaved by a second RNase III enzyme, called Dicer, which removes the terminal loop to generate the miRNA duplex intermediate. One strand of this duplex is incorporated into the RNA-induced silencing complex (RISC), where it acts as a guide RNA to direct RISC to complementary mRNA species [1]. Depending on the level of complementarity, RISC can either cleave bound mRNAs and/or inhibit their translation. Inhibition of mRNA translation generally requires full complementarity of the mRNA to nucleotides 2 through 7 or 8 from the miRNA 5′ end–the miRNA seed region. The primary, and possibly sole, function of mammalian miRNAs is therefore to act as specific post-transcriptional inhibitors of mRNA function.

Will Widgets and Semantic Tagging Change Computational Biology?:

We argue here, through the use of several examples from our work in support of structural biology, that the answer to the question posed by the title of this Perspective is a resounding yes. The discussion that follows is aimed primarily at those of the journal’s readers who are biological resource developers and Web page developers interested in developing the richest possible Web pages. However, those of you who simply use biological resources might find this a helpful discussion in understanding what is on the horizon. Whatever your interest, please let us hear your opinion on the question posed by this Perspective through the associated comment feature.

The Shifting Demographic Landscape of Pandemic Influenza:

As Pandemic (H1N1) 2009 influenza spreads around the globe, it strikes school-age children more often than adults. Although there is some evidence of pre-existing immunity among older adults, this alone may not explain the significant gap in age-specific infection rates. Based on a retrospective analysis of pandemic strains of influenza from the last century, we show that school-age children typically experience the highest attack rates in primarily naive populations, with the burden shifting to adults during the subsequent season. Using a parsimonious network-based mathematical model which incorporates the changing distribution of contacts in the susceptible population, we demonstrate that new pandemic strains of influenza are expected to shift the epidemiological landscape in exactly this way. Our analysis provides a simple demographic explanation for the age bias observed for H1N1/09 attack rates, and suggests that this bias may shift in coming months. These results have significant implications for the allocation of public health resources for H1N1/09 and future influenza pandemics.

Clock Quotes

By the time a man realizes that maybe his father was right, he usually has a son who thinks he’s wrong.
– Charles Wadsworth

2010 Research Blogging Awards finalists announced!

A stellar line-up of judges has finished their work and announced the finalists of the 2010 Research Blogging Awards. This was a huge job – just look at the entire list of nominees!!! What a fantastic list of the best of the best of science blogs and their best posts, in several languages.
You can see who made it to the finals by clicking here and start exploring blogs you did not know before. I guarantee you will find new candidates for your blogrolls and subscriptions.
Voting for the winners will be on March 4th and the winners of the awards will be announced on March 23rd.
I did make it in a couple of categories: ‘Best Blog — Biology’ and ‘Research Twitterer of the Year’, so I can proudly embed this logo/button here:
Research Blogging Awards 2010 Finalist
Congratulations to all the finalists – what a great collection of amazing writers!

Some AAAS links

Links in this post are those that pertain to me or the session I was in – I will link to some others later (and I already did on Twitter):
Columbia Journalism Review: Online and Overseas: Less hand-wringing over state of science journalism
Physicsworld.com: Researchers! Join the Twitterati! Or perish!
Thoughts From Kansas: AAAS Day 3: Social media in science
Scientificblogging.com: Science Journalists Have Met The Enemy, And They Are Bloggers
UC San Diego’s Jacobs School of Engineering: Interesting session at AAAS
john hawks weblog: AAAS
A Blog Around The Clock: AAAS 2010 meeting – the Press Room….why?
Interesting how each of these posts has its own spin and neither one of them actually describes the session and all the six panelists and what we said….perhaps later someone will do that.

ScienceOnline2010 – interview with Fabiana Kubke

Continuing with the tradition from last two years, I will occasionally post interviews with some of the participants of the ScienceOnline2010 conference that was held in the Research Triangle Park, NC back in January. See all the interviews in this series here. You can check out previous years’ interviews as well: 2008 and 2009.
Today, I asked Fabiana Kubke, who came to the conference all the way from New Zealand, to answer a few questions. Fabiana writes on Building Blogs of Science which is syndicated on SciBlogs.co.nz
Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your (scientific) background?
Kubke-Bora2.jpgI grew up in Argentina, where I did a Biology degree at the University of Buenos Aires and started working on developmental neurobiology. I then got the chance to do a PhD at the University of Connecticut (also in developmental neurobiology) after which I went to the University of Maryland to do a post-doc in neuroethology (barn owls sound localisation). There in Maryland I met Martin Wild who was doing a sabbatical, and asked me if I would consider moving to New Zealand to work with him. Next think I knew, all of my stuff was on a ship headed to the South Pacific and I had a one way ticket to New Zealand. Martin gave me the physical and intellectual space to become independent PI, and after many (emphasis on many) years of being on soft money I am now a Senior Lecturer (like an Assistant Prof) at Auckland. I love the research as much as I love the teaching and student supervision. I learn a lot from my students, they always manage to keep me on my toes and challenge my way of thinking.
Tell us a little more about your career trajectory so far: interesting projects past and present?
The main intellectual driving force for me has been to understand how brain circuits change during evolution to give rise to different behaviours. So I have always been jumping around different aspects of the problem (comparative embryology, anatomy, physiology), which means working with lots of collaborators. I mainly focus on the auditory system of birds because since vocal communication is so crucial in reproduction then vocal signals need to be well represented in the brain. The other advantage with working with birds is that many behaviours that are thought to be ‘of the human domain’ (like mirror recognition, episodic memory, tool manufacture) are also expressed in birds (just not all in a single species). This means comparative anatomy can provide nice cues as to what a circuit needs to have to get those behaviours expressed.
What is taking up the most of your time and passion these days? What are your goals?
Oh, heaps of stuff. After attending Kiwi Foo Camp in 2009, I got engaged with a great local community that wants to make things happen. It blew my mind. I found myself thinking a lot more about primary and secondary science education, Open Data, Open Science, etc. Not that it wasn’t in my mind before, but now it was around navigating how to make things happen. I became more actively involved in the discussions and that started challenging the way I do things. And I became less shy about seeking advise and doing stuff that are not the typical thing for an academic (like SciBarCamp, Science Online 2010, a Science Communication conference, the OLPC programme, etc). I am still mainly doing research, teaching and training, but I am spending heaps more time thinking about the ‘how’ and ‘why’. I would love a few years from now to look back and see that I have changed my ways to contribute to a better scientific environment. The main challenge for now is to keep an eye so that I can maintain a good bite:chew ratio.
What aspect of science communication and/or particular use of the Web in science interests you the most?
A friend of mine from Uni in Argentina (Diego Golombek) does a lot of popular science stuff back home, and I always quietly envied him. I looked into starting a local series of popular science books in New Zealand similar to his, but kept hitting walls and never got the project off. Then I met Peter Griffin from the Science Media Centre, and next thing I knew I was writing a blog. It changed the way I read science altogether, and the way I think about it. Then soon after, the opportunity to start a Citizen Science project came up and we set it up online. The web provides a great platform to build bridges between scientists, between scientists and the community and to demystify science (and scientists!). And I hope I can be a part of that process.
How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, FriendFeed and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?
When I was a Uni student in Argentina, the country was transitioning between the dictatorship and the new democracy. There was a lot of soul searching on what was the role of a free (as in no student fees) and autonomous university in society, and what was our responsibilities as scientists. My generation started their scientific careers with these issues in mind. I see some of the same issues being raised in social networks, this time around the issues of Open Science and Open Access. Most of these discussions I follow on FriendFeed. I leave Facebook for family and friends. On Twitter, I tend to follow a more diverse group, and a lot of people interested in OSS, open government, education. Social networks have become sort of a lifeline to me, and people’s generosity with their ideas and support never ceases to amaze me. I am lucky enough to find people to follow that are motivated, energetic and courageous about building a better system, even if it is by making small changes in their specific area. The discussions are always stimulating, and I am always learning and discovering something new.
When and how did you first discover science blogs? What are some of your favourites? Have you discovered any cool science blogs by the participants at the Conference?
I don’t really know; in my mind it is as if they have always been there. I guess I first came across them through topical google searches, and slowly built a list of blogs to follow. I am actually surprised when I find one I haven’t seen before, but every now and then it happens (as when going through the scio10 list). I have to say that my favourite blog is Ed Yong’s (the boy can write!). But my favourites tend to shift depending on what is occupying my mind at a given time. The great thing about scienceblogs is that I am always able to find a blog to help me think through any issue. New Zealand is a small country, and as a result the scientific community is small. It is hard to travel to meetings or invite speakers from abroad, so blogs (well, the bloggers really) take on a crucial role in providing me with a lot of food for thought.
What was the best aspect of ScienceOnline2010 for you? Any suggestions for next year? Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?
I think it was great to share the room with a lot of the people I follow online, and to have awesome chats with some of them. (Of course I felt it was too short to talk to everyone I wanted to talk to!). I would love to see more round table discussions rather than presentations. I still got heaps of feedback on ideas I have been toying around with, enjoyed hearing more about other Citizen Science projects, and left with a much better understanding of the science communication community. One specific thing, is that after chatting with Steve Koch, he got me to be invited to be an academic editor for PLoS One (for which I am very grateful). Cameron Neylon alerted me to the fact that UK universities are considered ‘commercial’ (so I changed my blog license). Overall, the big take home message for me was that even the great writers in the room started by learning how to communicate. And that means read/study/read/study/write. So I am doing a lot more studying these days, and hoping to use a lot of what I learn in also becoming a better lecturer.
It was so nice to see you and thank you for the interview. I hope to see you again next January.
Kubke-Bora1.jpg

ScienceOnline2010 – Journalists: What Scientists to Trust? (video) Part 4

How does a journalist figure out ‘which scientists to trust’?
Saturday, January 16 at 3:15 – 4:20pm
D. How does a journalist figure out “which scientists to trust”? – Christine Ottery and Connie St Louis
Description: We will talk about how science journalists can know which scientists to trust based on a blogpost by Christine Ottery that made a splash in the world of science communication. As a relative newcomer to science journalism and blogging (Christine) and an award-winning broadcaster, journalist, writer and scientist (Connie), we will be bringing two very different viewpoints to the discussion. We will be touching on peer review, journals, reputation and maverick scientists. We will also examine how journalists and scientists can foster good working relationships with each other, find out what is best practice when it comes to sources for science journalists, and turn the premise of the talk on its head and ask “Which journalists can you trust?” of the scientists.

New and Exciting in PLoS ONE

There are 21 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:
Vertebrate DNA in Fecal Samples from Bonobos and Gorillas: Evidence for Meat Consumption or Artefact?:

Deciphering the behavioral repertoire of great apes is a challenge for several reasons. First, due to their elusive behavior in dense forest environments, great ape populations are often difficult to observe. Second, members of the genus Pan are known to display a great variety in their behavioral repertoire; thus, observations from one population are not necessarily representative for other populations. For example, bonobos (Pan paniscus) are generally believed to consume almost no vertebrate prey. However, recent observations show that at least some bonobo populations may consume vertebrate prey more commonly than previously believed. We investigated the extent of their meat consumption using PCR amplification of vertebrate mitochondrial DNA (mtDNA) segments from DNA extracted from bonobo feces. As a control we also attempted PCR amplifications from gorilla feces, a species assumed to be strictly herbivorous. We found evidence for consumption of a variety of mammalian species in about 16% of the samples investigated. Moreover, 40% of the positive DNA amplifications originated from arboreal monkeys. However, we also found duiker and monkey mtDNA in the gorilla feces, albeit in somewhat lower percentages. Notably, the DNA sequences isolated from the two ape species fit best to the species living in the respective regions. This result suggests that the sequences are of regional origin and do not represent laboratory contaminants. Our results allow at least three possible and mutually not exclusive conclusions. First, all results may represent contamination of the feces by vertebrate DNA from the local environment. Thus, studies investigating a species’ diet from feces DNA may be unreliable due to the low copy number of DNA originating from diet items. Second, there is some inherent difference between the bonobo and gorilla feces, with only the later ones being contaminated. Third, similar to bonobos, for which the consumption of monkeys has only recently been documented, the gorilla population investigated (for which very little observational data are as yet available) may occasionally consume small vertebrates. Although the last explanation is speculative, it should not be discarded a-priori given that observational studies continue to unravel new behaviors in great ape species.

Continue reading