A Blog Around The Clock

Pets Teach Science: 16 golden retrievers explain atoms (video)

Fri, 20 Nov 2009 18:45:30 -0500

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Today's carnivals

Fri, 20 Nov 2009 14:40:46 -0500

The 124th Meeting Of The Skeptics' Circle is up on Beyond the Short Coat

Friday Ark #270 is up on Modulator

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ScienceOnline2010 - introducing the participants

Fri, 20 Nov 2009 12:06:05 -0500

As you know you can see everyone who's registered for the conference, but I highlight 4-6 participants every day as this may be an easier way for you to digest the list. You can also look at the Program so see who is doing what.

Hope Leman is a Research Information Technologist at Samaritan Health Services. She runs ScanGrants (a free, subscribable (via email or RSS) online listing of grant opportunities, prizes and scholarships in the health and life sciences and community service fields), tweets and blogs on Significant Science. At the conference, Hope will do a demo of ScanGrants.

Ernie Hood is a freelance science writer and he hosts a weekly science radio show - Radio In Vivo - at the local radio station WCOM-FM in Carrboro, NC. Ernie is currently presiding over SCONC - the organization of Science Communicators of North Carolina.

Elle Cayabyab Gitlin writes for Ars Technica, blogs and tweets. And she is always a great help to us at the conference, every year volunteering to help.

Peter Janiszewski is an Obesity Researcher (PhD Candidate) in the Exercise Physiology Lab at Queen's University, Ontario, Canada, a Science/Health Blogger at Obesity Panacea, a freelance writer, a musician, and a Twitterer.

Jayme Corbell, another veteran of our conferences, got her PhD in chemistry at Duke and now works at Catalent.

Jonathan Lifland is the Media and Communications Manager at PNAS (Proceedings of the National Academy of Sciences) and is on Twitter

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Museum lecture traces historic Beagle voyage

Fri, 20 Nov 2009 10:14:48 -0500

The North Carolina Museum of Natural Sciences hosts the final offering of its Charles Darwin Lecture Series on Tuesday, November 24 -- the 150th anniversary of Darwin's landmark publication of "The Origin of Species." Join Museum paleontologist and science historian Paul Brinkman for a free presentation titled "Charles Darwin's Beagle Voyage and the Origin of 'The Origin.'"
Dr. Brinkman completed his PhD in History of Science at the University of Minnesota with research in the history of 19th-century natural sciences, especially geology and paleontology. He has published a number of articles on Darwin, museum history, and the history of American vertebrate paleontology. His second book, The Second American Jurassic Dinosaur Rush, is due out next year from the University of Chicago Press.

Please RSVP to museum.reservations@ncmail.net -- be sure to specify the event name and date. This lecture is free of charge and seating is on a first-come, first-served basis. Doors to the Museum and auditorium will open at 6:00 pm and the presentation will begin at 6:30 pm.

The Museum, in collaboration with the National Evolutionary Synthesis Center (NESCent) and the W.M. Keck Center for Behavioral Biology at North Carolina State University, has presented several talks throughout 2009 to commemorate the bicentennial of Charles Darwin's birth and the 150th anniversary of the publication of "The Origin of Species." The series showcases the Triangle region of North Carolina as a hot spot for evolutionary biology research and features prominent researchers from area universities. Stay tuned to the Museum's website [www.naturalsciences.org] for Darwin-themed events scheduled for 2010.

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New and Exciting in PLoS this week

Fri, 20 Nov 2009 08:54:07 -0500

Friday - PLoS Genetics, Pathogens, Computational Biology and ONE published 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:

Circadian KaiC Phosphorylation: A Multi-Layer Network:

Circadian clocks are endogenous timing mechanisms that allow living organisms to coordinate their activities with daily environmental fluctuations. In cyanobacteria, almost all the genes are rhythmically expressed with the same ~24 h period yet exhibit a variety of phase relationships and waveforms. Remarkably, the core pacemaker ticks robustly via simple biochemical reactions carried out by three Kai proteins: KaiC undergoes circadian phosphorylation in the presence of KaiA, KaiB and ATP. In this work, we propose a reaction network modeling the Kai oscillator based on the differentiation of dual phosphorylation sites. We found a dynamic diversity in KaiC phosphorylation which may serve as a potential regulatory mechanism related to the diverse-phased genome-wide expressions in cyanobacteria. In addition, we deduce that each KaiC hexamer is a single oscillator in regulating its own phosphorylation and interactions with KaiA or/and KaiB. In complex organisms, a number of key clock components possess similar activities (e.g., phosphorylation) with multiple nonequivalent active sites, and they may also show some unusual dynamic features that are embedded in the proteins' own reaction networks. We hope our work could be helpful to study the correlations between gene expressions and circadian rhythm in prokaryotic cells, even in eukaryotic cells.

Evaluation of the Oscillatory Interference Model of Grid Cell Firing through Analysis and Measured Period Variance of Some Biological Oscillators:

For many animals, including rats, accurate spatial memory over relatively large areas is important in order to find food and shelter. Just as unique points in time can be efficiently represented by combinations of repeating elements like hours, days, and months, points in space can be represented as combinations of elements that repeat at different spatial scales. Just such a code has been identified in the brains of rats and it shows an intriguing triangular spacing of encoded locations. Two different explanations have been developed as to what general mechanism in the brain might be able to generate this unusual code. However, to date there is not conclusive experimental evidence indicating whether either of the two explanations is correct. Here we show in detail that one of the explanations, called oscillatory interference, has specific requirements regarding the amount of variability in the system that implements it. We then report data experimentally examining candidate systems to evaluate their levels of noise. The large amount of noise that we find presents a challenge to the currently suggested biological implementations of oscillatory interference, but it does not provide support for the alternative explanation.

10 Reasons to be Tantalized by the B73 Maize Genome:

Why should you read about the maize genome? Now that so many eukaryotic genomes are available, it's easy to be blasé... just another few billion bases, grist for constructing gene trees. Why is this new information, so recently shared, worth considering? I am convinced, as I propose you will be too as you read on, that both geneticists and genome consumers will benefit from the first description of the B73 maize genome [1] and equally so from the companion papers compiled in this special collection (http://collections.plos.org/plosgenetics/maize.php ).

On Theoretical Models of Gene Expression Evolution with Random Genetic Drift and Natural Selection:

The relative contributions of natural selection and random genetic drift are a major source of debate in the study of gene expression evolution, which is hypothesized to serve as a bridge from molecular to phenotypic evolution. It has been suggested that the conflict between views is caused by the lack of a definite model of the neutral hypothesis, which can describe the long-run behavior of evolutionary change in mRNA abundance. Therefore previous studies have used inadequate analogies with the neutral prediction of other phenomena, such as amino acid or nucleotide sequence evolution, as the null hypothesis of their statistical inference. In this study, we introduced two novel theoretical models, one based on neutral drift and the other assuming natural selection, by focusing on a common property of the distribution of mRNA abundance among a variety of eukaryotic cells, which reflects the result of long-term evolution. Our results demonstrated that (1) our models can reproduce two independently found phenomena simultaneously: the time development of gene expression divergence and Zipf's law of the transcriptome; (2) cytological constraints can be explicitly formulated to describe long-term evolution; (3) the model assuming that natural selection optimized relative mRNA abundance was more consistent with previously published observations than the model of optimized absolute mRNA abundances. The models introduced in this study give a formulation of evolutionary change in the mRNA abundance of each gene as a stochastic process, on the basis of previously published observations. This model provides a foundation for interpreting observed data in studies of gene expression evolution, including identifying an adequate time scale for discriminating the effect of natural selection from that of random genetic drift of selectively neutral variations.

Combination of Real-Value Smell and Metaphor Expression Aids Yeast Detection:

Smell provides important information about the quality of food and drink. Most well-known for their expertise in wine tasting, sommeliers sniff out the aroma of wine and describe them using beautiful metaphors. In contrast, electronic noses, devices that mimic our olfactory recognition system, also detect smells using their sensors but describe them using electronic signals. These devices have been used to judge the freshness of food or detect the presence of pathogenic microorganisms. However, unlike information from gas chromatography, it is difficult to compare odour information collected by these devices because they are made for smelling specific smells and their data are relative intensities. Here, we demonstrate the use of an absolute-value description method using known smell metaphors, and early detection of yeast using the method. This technique may help distinguishing microbial-contamination of food products earlier, or improvement of the food-product qualities.

Motor and Linguistic Linking of Space and Time in the Cerebellum:

Recent literature documented the presence of spatial-temporal interactions in the human brain. The aim of the present study was to verify whether representation of past and future is also mapped onto spatial representations and whether the cerebellum may be a neural substrate for linking space and time in the linguistic domain. We asked whether processing of the tense of a verb is influenced by the space where response takes place and by the semantics of the verb. Responses to past tense were facilitated in the left space while responses to future tense were facilitated in the right space. Repetitive transcranial magnetic stimulation (rTMS) of the right cerebellum selectively slowed down responses to future tense of action verbs; rTMS of both cerebellar hemispheres decreased accuracy of responses to past tense in the left space and to future tense in the right space for non-verbs, and to future tense in the right space for state verbs. The results suggest that representation of past and future is mapped onto spatial formats and that motor action could represent the link between spatial and temporal dimensions. Right cerebellar, left motor brain networks could be part of the prospective brain, whose primary function is to use past experiences to anticipate future events. Both cerebellar hemispheres could play a role in establishing the grammatical rules for verb conjugation.

Genome-Wide Scan for Signatures of Human Population Differentiation and Their Relationship with Natural Selection, Functional Pathways and Diseases:

Genetic differences both between individuals and populations are studied for their evolutionary relevance and for their potential medical applications. Most of the genetic differentiation among populations are caused by random drift that should affect all loci across the genome in a similar manner. When a locus shows extraordinary high or low levels of population differentiation, this may be interpreted as evidence for natural selection. The most used measure of population differentiation was devised by Wright and is known as fixation index, or FST. We performed a genome-wide estimation of FST on about 4 millions of SNPs from HapMap project data. We demonstrated a heterogeneous distribution of FST values between autosomes and heterochromosomes. When we compared the FST values obtained in this study with another evolutionary measure obtained by comparative interspecific approach, we found that genes under positive selection appeared to show low levels of population differentiation. We applied a gene set approach, widely used for microarray data analysis, to detect functional pathways under selection. We found that one pathway related to antigen processing and presentation showed low levels of FST, while several pathways related to cell signalling, growth and morphogenesis showed high FST values. Finally, we detected a signature of selection within genes associated with human complex diseases. These results can help to identify which process occurred during human evolution and adaptation to different environments. They also support the hypothesis that common diseases could have a genetic background shaped by human evolution.

A Mechanistic Niche Model for Measuring Species' Distributional Responses to Seasonal Temperature Gradients:

Niche theory is central to understanding how species respond geographically to climate change. It defines a species' realized niche in a biological community, its fundamental niche as determined by physiology, and its potential niche--the fundamental niche in a given environment or geographic space. However, most predictions of the effects of climate change on species' distributions are limited to correlative models of the realized niche, which assume that species are in distributional equilibrium with respect to the variables or gradients included in the model. Here, I present a mechanistic niche model that measures species' responses to major seasonal temperature gradients that interact with the physiology of the organism. I then use lethal physiological temperatures to parameterize the model for bird species in North and South America and show that most focal bird species are not in direct physiological equilibrium with the gradients. Results also show that most focal bird species possess broad thermal tolerances encompassing novel climates that could become available with climate change. I conclude with discussion of how mechanistic niche models may be used to (i) gain insights into the processes that cause species to respond to climate change and (ii) build more accurate correlative distribution models in birds and other species.

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Clock Quotes

Fri, 20 Nov 2009 03:46:50 -0500

America is a large friendly dog in a small room. Every time it wags its tail it knocks over a chair.

- Arnold Joseph Toynbee

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ScienceOnline2010 - introducing the participants

Thu, 19 Nov 2009 09:49:35 -0500

Continuing with the series (I get more and more feedback that people love this) introducing, a few at a time, the participants of the ScienceOnline2010 conference. You can also look at the Program so see who is doing what.

Anil Dash is a pioneer blogger (and of course twitterer) and one of the founders of Six Apart, the company that built blogging platforms including MoveableType (which is used by Scienceblogs.com) and Typepad.

Just yesterday, he made an official announcement that he will be leading Expert Labs (also on Twitter) which is a new project (largely run/funded by AAAS) to facilitate feedback by the experts (including scientists, of course) to the Obama Administration and other government officials. Read the press release, the early media coverage (this one is much better) , an interview with Anil (pdf) and a video. Interestingly, Anil got this job due to writing a blog post stating that the executive branch of the federal government of the United States was the "Most Interesting New Tech Startup of 2009".

At ScienceOnline2010, Anil will run the session Government 2.0 the main purpose of which is for him to get feedback from the leaders of the science and Web community on how to make Expert Labs work the best it possibly can.

Lindsey Hoshaw is a freelance journalist and a recent journalism graduate from Stanford University. She has stirred quite a lot of passion in the world of journalism recently by being one of the first and probably best known products of 'crowdsourced journalism' - she made a pitch at Spot.us and it was successful - she collected sufficient funds (and the Facebook fan page helped there as well) to go on a reporting trip on a research ship to the Great Pacific Garbage Patch. She reported from the voyage on her blog and via Twitter (also her personal account). I blogged about this before the trip started.

A short summary article by Lindsey was then published in the New York Times (which, while making no promises, was interested in the story from the start). That article (and especially in comparison to her blogging) was greeted by quite a lot of commentary, some by media watchers and journalists, some by scientists. See the reactions, for example, by Megan Garber, Miriam Goldstein, John Zhu, Martin Robbins, Mathew Ingram and Sheril Kirshenbaum (and Sheril again - read the comment thread).

The voyage, and the reporting from it (both on traditional and modern media platforms), brought into light the differences between the goals, needs, methods and ethics of journalists and those of scientists. What those differences are, and how they can be surmounted so scientists and journalists can work together and each do a better job, will be the topic of the session that Lindsay will be co-moderating - Talking Trash - which promises to be quite exciting!

Ben MacNeill is a designer here in Chapel Hill. I first met Ben at the 2005 BloggerCon at UNC. When his daughter Trixie was born he started a blog, Trixie Update, on which he recorded and graphed everything he could think of about his daughter's daily patterns: when she slept, ate, had a diaper change, etc. I commented on this, from a perspective of a chronobiologist, in an old blog post about the development and consolidation of circadian rhythms and sleep patterns in human infants. Trixie is far too old to have diapers changed any more, but the setup continues. Ben has developed the software further and is now offering it as an iPhone (or Web) application - the Trixie Tracker which you can use, if you are a new parent, to track everything you want about your baby (and perhaps detect early if something suddenly changes and perhaps requires medical attention). Ben is also on Twitter.

At the conference, Ben will do a demo of Data-driven parenting - Trixie Tracker and co-moderate the session on Citizen Science.

Elia Ben-Ari is a freelance science writer and editor who has published in many good venues over the years. She is active on Twitter. Her latest article (which, understandably, garnered quite a lot of interest online) is Twitter: What's All the Chirping About?

Wayne Sutton is a social media maven. He is a partner of social media marketing agency OurHashtag, the co-host of a social media podcast at TalkSocialNews.com, the host of the online video show WayneSutton.TV, and a veteran blogger. He is on every social networking site imaginable, but here let's just link to his Twitter account. At ScienceOnline2010, Wayne will do an Ignite talk "Why Triangle is Better than Silicon Valley".

Cara Rousseau is the Director for Partnership Initiatives at the Research Triangle Foundation (read more about it in yesterday's post), one of our biggest sponsors and hosts this year. She tweets, both as herself and for RTP and has just started the official RTP blog. At the conference, Cara will do a demo of the Research Triangle Park - how online and offline work together.

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New and Exciting in PLoS ONE

Thu, 19 Nov 2009 09:11:09 -0500

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:

The Astronomical Orientation of Ancient Greek Temples:

Despite its appearing to be a simple question to answer, there has been no consensus as to whether or not the alignments of ancient Greek temples reflect astronomical intentions. Here I present the results of a survey of archaic and classical Greek temples in Sicily and compare them with temples in Greece. Using a binomial test I show strong evidence that there is a preference for solar orientations. I then speculate that differences in alignment patterns between Sicily and Greece reflect differing pressures in the expression of ethnic identity.

Distributed Network, Wireless and Cloud Computing Enabled 3-D Ultrasound; a New Medical Technology Paradigm:

Medical technologies are indispensable to modern medicine. However, they have become exceedingly expensive and complex and are not available to the economically disadvantaged majority of the world population in underdeveloped as well as developed parts of the world. For example, according to the World Health Organization about two thirds of the world population does not have access to medical imaging. In this paper we introduce a new medical technology paradigm centered on wireless technology and cloud computing that was designed to overcome the problems of increasing health technology costs. We demonstrate the value of the concept with an example; the design of a wireless, distributed network and central (cloud) computing enabled three-dimensional (3-D) ultrasound system. Specifically, we demonstrate the feasibility of producing a 3-D high end ultrasound scan at a central computing facility using the raw data acquired at the remote patient site with an inexpensive low end ultrasound transducer designed for 2-D, through a mobile device and wireless connection link between them. Producing high-end 3D ultrasound images with simple low-end transducers reduces the cost of imaging by orders of magnitude. It also removes the requirement of having a highly trained imaging expert at the patient site, since the need for hand-eye coordination and the ability to reconstruct a 3-D mental image from 2-D scans, which is a necessity for high quality ultrasound imaging, is eliminated. This could enable relatively untrained medical workers in developing nations to administer imaging and a more accurate diagnosis, effectively saving the lives of people.

Generation and Characterization of Fmr1 Knockout Zebrafish:

Fragile X syndrome (FXS) is one of the most common known causes of inherited mental retardation. The gene mutated in FXS is named FMR1, and is well conserved from human to Drosophila. In order to generate a genetic tool to study FMR1 function during vertebrate development, we generated two mutant alleles of the fmr1 gene in zebrafish. Both alleles produce no detectable Fmr protein, and produce viable and fertile progeny with lack of obvious phenotypic features. This is in sharp contrast to published results based on morpholino mediated knock-down of fmr1, reporting defects in craniofacial development and neuronal branching in embryos. These phenotypes we specifically addressed in our knock-out animals, revealing no significant deviations from wild-type animals, suggesting that the published morpholino based fmr1 phenotypes are potential experimental artifacts. Therefore, their relation to fmr1 biology is questionable and morpholino induced fmr1 phenotypes should be avoided in screens for potential drugs suitable for the treatment of FXS. Importantly, a true genetic zebrafish model is now available which can be used to study FXS and to derive potential drugs for FXS treatment.

Emotional Modulation of Attention: Fear Increases but Disgust Reduces the Attentional Blink:

It is well known that facial expressions represent important social cues. In humans expressing facial emotion, fear may be configured to maximize sensory exposure (e.g., increases visual input) whereas disgust can reduce sensory exposure (e.g., decreases visual input). To investigate whether such effects also extend to the attentional system, we used the "attentional blink" (AB) paradigm. Many studies have documented that the second target (T2) of a pair is typically missed when presented within a time window of about 200-500 ms from the first to-be-detected target (T1; i.e., the AB effect). It has recently been proposed that the AB effect depends on the efficiency of a gating system which facilitates the entrance of relevant input into working memory, while inhibiting irrelevant input. Following the inhibitory response on post T1 distractors, prolonged inhibition of the subsequent T2 is observed. In the present study, we hypothesized that processing facial expressions of emotion would influence this attentional gating. Fearful faces would increase but disgust faces would decrease inhibition of the second target. We showed that processing fearful versus disgust faces has different effects on these attentional processes. We found that processing fear faces impaired the detection of T2 to a greater extent than did the processing disgust faces. This finding implies emotion-specific modulation of attention. Based on the recent literature on attention, our finding suggests that processing fear-related stimuli exerts greater inhibitory responses on distractors relative to processing disgust-related stimuli. This finding is of particular interest for researchers examining the influence of emotional processing on attention and memory in both clinical and normal populations. For example, future research could extend upon the current study to examine whether inhibitory processes invoked by fear-related stimuli may be the mechanism underlying the enhanced learning of fear-related stimuli.

Synergy between Repellents and Organophosphates on Bed Nets: Efficacy and Behavioural Response of Natural Free-Flying An. gambiae Mosquitoes:

Chemicals are used on bed nets in order to prevent infected bites and to kill aggressive malaria vectors. Because pyrethroid resistance has become widespread in the main malaria vectors, research for alternative active ingredients becomes urgent. Mixing a repellent and a non-pyrethroid insecticide seemed to be a promising tool as mixtures in the laboratory showed the same features as pyrethroids. We present here the results of two trials run against free-flying Anopheles gambiae populations comparing the effects of two insect repellents (either DEET or KBR 3023, also known as icaridin) and an organophosphate insecticide at low-doses (pirimiphos-methyl, PM) used alone and in combination on bed nets. We showed that mixtures of PM and the repellents induced higher exophily, blood feeding inhibition and mortality among wild susceptible and resistant malaria vectors than compounds used alone. Nevertheless the synergistic interactions are only involved in the high mortality induced by the two mixtures. These field trials argue in favour of the strategy of mixing repellent and organophosphate on bed nets to better control resistant malaria vectors.

Survival and Cardioprotective Benefits of Long-Term Blueberry Enriched Diet in Dilated Cardiomyopathy Following Myocardial Infarction in Rats:

Despite remarkable progress in treatment of chronic heart failure (CHF) over the last two decades, mortality, personal suffering and cost remain staggering, and effective interventions are still a challenge. Previously we reported that a blueberry-enriched diet (BD) attenuated necroapoptosis and inflammation in periinfarct area in a rat model of myocardial infarction (MI). To test the hypothesis that BD will attenuate the course of CHF, including mortality and cardiac remodeling during the first year after induction of MI in rats. Two weeks after coronary artery ligation, rats were divided into two groups of similar average MI size, measured by echocardiography, and then12-mo dietary regimens were initiated as follows: ad libitum regular diet (control, CD, n = 27) and isocaloric food with 2% blueberry supplement (BD, n = 27) also available ad libitum. These dietary groups were compared to each other and to sham group (SH). Mortality over the 12 mo was reduced by 22% in BD compared with CD (p<0.01). In the course of developing CHF, BD had no effect on the body weight, heart rate or blood pressure. Bi-monthly Echo revealed significant attenuation of the LV chamber remodeling, LV posterior wall thinning, and MI expansion in BD compared with CD. In fact, BD arrested the MI expansion. This is the first experimental evidence that a blueberry-enriched diet has positive effects on the course of CHF and thus warrants consideration for clinical evaluation.

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Clock Quotes

Thu, 19 Nov 2009 03:59:39 -0500

Success is simple. Do what's right, the right way, at the right time.

- Arnold H. Glasgow

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Celebrate Darwin's 200th birthday

Wed, 18 Nov 2009 12:57:23 -0500

NESCent and SCONC:

What: November SCONC-fest
When: Thursday November 19th , 6-8pm

Where: National Evolutionary Synthesis Center in Durham

Please join us to commemorate Charles Darwin's 200th birthday and the 150th anniversary of "The Origin of Species."

Learn about the wild world of Ice Age carnivores, brainy birds, and other creatures Darwin missed. Our tour guides will be four postdocs on the frontiers of biology.

We'll begin at 6pm at the National Evolutionary Synthesis Center in Durham. Parking is free.

National Evolutionary Synthesis Center (NESCent)
2024 W. Main Street, Suite A200
Durham, NC 27705

Map: http://bit.ly/rGmKM

Travel Directions: The National Evolutionary Synthesis Center is near the corner of 9th St. and W. Main St. in Durham, on the 2nd floor of the Erwin Mill Building. Free parking is available in front of the building.

To RSVP please drop a note to: rsmith@nescent.org

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ScienceOnline2010 - introducing the participants

Wed, 18 Nov 2009 10:09:55 -0500

I have to say I am myself enjoying doing these introductory posts. I get to Google people, see who they are and what they've been up to lately, discover stuff about friends' past careers I did not know, find them (and follow/subscribe/friend) on Twitter, FriendFeed and Facebook, and generally get all starry-eyed about the amazing group of people who registered for the conference and who I can't wait to see. So, without further ado, here are a few more of them:

Beth Beck is the Outreach Program Manager for Space Operations at NASA Headquarters in Washington DC. And no, she is not a rocket scientist, she is a political scientist. She blogs and tweets. At the conference, Beth will co-moderate the session Broader Impact Done Right.

Henry Gee is a Senior Editor at Nature, founder and editor of Nature Futures, columnist on BBC Focus, editor of Mallorn (journal of the Tolkien Society), writer and editor of several science and SF books, a compulsive twitterer as well as a blogger both on I, Editor and The End Of The Pier Show. And a dear personal friend.

Connie St Louis is the Director of the Science Journalism MA at City University, London. She is an award-winning freelance broadcaster, journalist, writer and scientist, noted for her work at BBC Radio 4 and BBC World Service. At the conference, Connie will co-moderate (together with her student Christine Ottery) the session How does a journalist figure out 'which scientists to trust'?

Michael Nitabach is the Assistant Professor of Cellular & Molecular Physiology at Yale School of Medicine, the Interdepartmental Neuroscience Program and the Department of Biological and Biomedical Sciences at Yale. And he is a colleague - an awesome chronobiologist.

Robin Ann Smith is the alumna of the Duke University Writing Program, a freelance science writer, and the Communications Manager (and official twitterer) at the National Evolutionary Synthesis Center (NESCent). At the conference, Robin will do a demo presentation of NESCent online efforts.

Josh Wilson is the Reference Librarian for Physical & Mathematical Sciences at the D.H.Hill library at NCSU, my alma mater. Josh blogs and tweets as well.

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New and Exciting in PLoS ONE

Wed, 18 Nov 2009 09:21:14 -0500

There are 28 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:

Breaking the News or Fueling the Epidemic? Temporal Association between News Media Report Volume and Opioid-Related Mortality:

Historical studies of news media have suggested an association between reporting and increased drug abuse. Period effects for substance use have been documented for different classes of legal and illicit substances, with the suspicion that media publicity may have played major roles in their emergence. Previous analyses have drawn primarily from qualitative evidence; the temporal relationship between media reporting volume and adverse health consequences has not been quantified nationally. We set out to explore whether we could find a quantitative relationship between media reports about prescription opioid abuse and overdose mortality associated with these drugs. We assessed whether increases in news media reports occurred before or after increases in overdose deaths. Our ecological study compared a monthly time series of unintentional poisoning deaths involving short-acting prescription opioid substances, from 1999 to 2005 using multiple cause-of-death data published by the National Center for Health Statistics, to monthly counts of English-language news articles mentioning generic and branded names of prescription opioids obtained from Google News Archives from 1999 to 2005. We estimated the association between media volume and mortality rates by time-lagged regression analyses. There were 24,272 articles and 30,916 deaths involving prescription opioids during the seven-year study period. Nationally, the number of articles mentioning prescription opioids increased dramatically starting in early 2001, following prominent coverage about the nonmedical use of OxyContin. We found a significant association between news reports and deaths, with media reporting preceding fatal opioid poisonings by two to six months and explaining 88% (p<0.0001, df 78) of the variation in mortality. While availability, structural, and individual predispositions are key factors influencing substance use, news reporting may enhance the popularity of psychoactive substances. Albeit ecological in nature, our finding suggests the need for further evaluation of the influence of news media on health. Reporting on prescription opioids conforms to historical patterns of news reporting on other psychoactive substances.

Rhesus Monkeys' Valuation of Vocalizations during a Free-Choice Task:

Adaptive behavior requires that animals integrate current and past information with their decision-making. One important type of information is auditory-communication signals (i.e., species-specific vocalizations). Here, we tested how rhesus monkeys incorporate the opportunity to listen to different species-specific vocalizations into their decision-making processes. In particular, we tested how monkeys value these vocalizations relative to the opportunity to get a juice reward. To test this hypothesis, monkeys chose one of two targets to get a varying juice reward; at one of those targets, in addition to the juice reward, a vocalization was presented. By titrating the juice amounts at the two targets, we quantified the relationship between the monkeys' juice choices relative to the opportunity to listen to a vocalization. We found that, rhesus were not willing to give up a large juice reward to listen to vocalizations indicating that, relative to a juice reward, listening to vocalizations has a low value.

The Typical Flight Performance of Blowflies: Measuring the Normal Performance Envelope of Calliphora vicina Using a Novel Corner-Cube Arena:

Despite a wealth of evidence demonstrating extraordinary maximal performance, little is known about the routine flight performance of insects. We present a set of techniques for benchmarking performance characteristics of insects in free flight, demonstrated using a model species, and comment on the significance of the performance observed. Free-flying blowflies (Calliphora vicina) were filmed inside a novel mirrored arena comprising a large (1.6 m1.6 m1.6 m) corner-cube reflector using a single high-speed digital video camera (250 or 500 fps). This arrangement permitted accurate reconstruction of the flies' 3-dimensional trajectories without the need for synchronisation hardware, by virtue of the multiple reflections of a subject within the arena. Image sequences were analysed using custom-written automated tracking software, and processed using a self-calibrating bundle adjustment procedure to determine the subject's instantaneous 3-dimensional position. We illustrate our method by using these trajectory data to benchmark the routine flight performance envelope of our flies. Flight speeds were most commonly observed between 1.2 ms−1 and 2.3 ms−1, with a maximum of 2.5 ms−1. Our flies tended to dive faster than they climbed, with a maximum descent rate (−2.4 ms−1) almost double the maximum climb rate (1.2 ms−1). Modal turn rate was around 240°s−1, with maximal rates in excess of 1700°s−1. We used the maximal flight performance we observed during normal flight to construct notional physical limits on the blowfly flight envelope, and used the distribution of observations within that notional envelope to postulate behavioural preferences or physiological and anatomical constraints. The flight trajectories we recorded were never steady: rather they were constantly accelerating or decelerating, with maximum tangential accelerations and maximum centripetal accelerations on the order of 3 g.

In-Group Conformity Sustains Different Foraging Traditions in Capuchin Monkeys (Cebus apella):

Decades of research have revealed rich cultural repertoires encompassing multiple traditions in wild great apes, a picture crucially complemented by experimental simulations with captive apes. Studies with wild capuchin monkeys, the most encephalized simian species, have indicated a New World convergence on these cultural phenomena, involving multiple traditions and tool use. However, experimental studies to date are in conflict with such findings in concluding that capuchins, like other monkeys, show minimal capacities for social learning. Here we report a new experimental approach in which the alpha male of each of two groups of capuchins was trained to open an artificial foraging device in a quite different way, using either a slide or lift action, then reunited with his group. In each group a majority of monkeys, 8 of 11 and 13 of 14, subsequently mastered the task. Seventeen of the successful 21 monkeys discovered the alternative action to that seeded in the group, performing it a median of 4 times. Nevertheless, all 21 primarily adopted the technique seeded by their group's alpha male. Median proportions of slide versus lift were 0.96 for the group seeded with slide versus 0. 01 for the group seeded with lift. These results suggest a striking effect of social conformity in learned behavioral techniques, consistent with field reports of capuchin traditions and convergent on the only other species in which such cultural phenomena have been reported, chimpanzees and humans.

The Real maccoyii: Identifying Tuna Sushi with DNA Barcodes - Contrasting Characteristic Attributes and Genetic Distances:

The use of DNA barcodes for the identification of described species is one of the least controversial and most promising applications of barcoding. There is no consensus, however, as to what constitutes an appropriate identification standard and most barcoding efforts simply attempt to pair a query sequence with reference sequences and deem identification successful if it falls within the bounds of some pre-established cutoffs using genetic distance. Since the Renaissance, however, most biological classification schemes have relied on the use of diagnostic characters to identify and place species. Here we developed a cytochrome c oxidase subunit I character-based key for the identification of all tuna species of the genus Thunnus, and compared its performance with distance-based measures for identification of 68 samples of tuna sushi purchased from 31 restaurants in Manhattan (New York City) and Denver, Colorado. Both the character-based key and GenBank BLAST successfully identified 100% of the tuna samples, while the Barcode of Life Database (BOLD) as well as genetic distance thresholds, and neighbor-joining phylogenetic tree building performed poorly in terms of species identification. A piece of tuna sushi has the potential to be an endangered species, a fraud, or a health hazard. All three of these cases were uncovered in this study. Nineteen restaurant establishments were unable to clarify or misrepresented what species they sold. Five out of nine samples sold as a variant of "white tuna" were not albacore (T. alalunga), but escolar (Lepidocybium flavorunneum), a gempylid species banned for sale in Italy and Japan due to health concerns. Nineteen samples were northern bluefin tuna (T. thynnus) or the critically endangered southern bluefin tuna (T. maccoyii), though nine restaurants that sold these species did not state these species on their menus. The Convention on International Trade Endangered Species (CITES) requires that listed species must be identifiable in trade. This research fulfills this requirement for tuna, and supports the nomination of northern bluefin tuna for CITES listing in 2010.

Nestedness of Ectoparasite-Vertebrate Host Networks:

Determining the structure of ectoparasite-host networks will enable disease ecologists to better understand and predict the spread of vector-borne diseases. If these networks have consistent properties, then studying the structure of well-understood networks could lead to extrapolation of these properties to others, including those that support emerging pathogens. Borrowing a quantitative measure of network structure from studies of mutualistic relationships between plants and their pollinators, we analyzed 29 ectoparasite-vertebrate host networks--including three derived from molecular bloodmeal analysis of mosquito feeding patterns--using measures of nestedness to identify non-random interactions among species. We found significant nestedness in ectoparasite-vertebrate host lists for habitats ranging from tropical rainforests to polar environments. These networks showed non-random patterns of nesting, and did not differ significantly from published estimates of nestedness from mutualistic networks. Mutualistic and antagonistic networks appear to be organized similarly, with generalized ectoparasites interacting with hosts that attract many ectoparasites and more specialized ectoparasites usually interacting with these same "generalized" hosts. This finding has implications for understanding the network dynamics of vector-born pathogens. We suggest that nestedness (rather than random ectoparasite-host associations) can allow rapid transfer of pathogens throughout a network, and expand upon such concepts as the dilution effect, bridge vectors, and host switching in the context of nested ectoparasite-vertebrate host networks.

Mutations in H5N1 Influenza Virus Hemagglutinin that Confer Binding to Human Tracheal Airway Epithelium:

The emergence in 2009 of a swine-origin H1N1 influenza virus as the first pandemic of the 21st Century is a timely reminder of the international public health impact of influenza viruses, even those associated with mild disease. The widespread distribution of highly pathogenic H5N1 influenza virus in the avian population has spawned concern that it may give rise to a human influenza pandemic. The mortality rate associated with occasional human infection by H5N1 virus approximates 60%, suggesting that an H5N1 pandemic would be devastating to global health and economy. To date, the H5N1 virus has not acquired the propensity to transmit efficiently between humans. The reasons behind this are unclear, especially given the high mutation rate associated with influenza virus replication. Here we used a panel of recombinant H5 hemagglutinin (HA) variants to demonstrate the potential for H5 HA to bind human airway epithelium, the predominant target tissue for influenza virus infection and spread. While parental H5 HA exhibited limited binding to human tracheal epithelium, introduction of selected mutations converted the binding profile to that of a current human influenza strain HA. Strikingly, these amino-acid changes required multiple simultaneous mutations in the genomes of naturally occurring H5 isolates. Moreover, H5 HAs bearing intermediate sequences failed to bind airway tissues and likely represent mutations that are an evolutionary "dead end." We conclude that, although genetic changes that adapt H5 to human airways can be demonstrated, they may not readily arise during natural virus replication. This genetic barrier limits the likelihood that current H5 viruses will originate a human pandemic.

Genetic Variation and Recent Positive Selection in Worldwide Human Populations: Evidence from Nearly 1 Million SNPs:

Genome-wide scans of hundreds of thousands of single-nucleotide polymorphisms (SNPs) have resulted in the identification of new susceptibility variants to common diseases and are providing new insights into the genetic structure and relationships of human populations. Moreover, genome-wide data can be used to search for signals of recent positive selection, thereby providing new insights into the genetic adaptations that occurred as modern humans spread out of Africa and around the world. We genotyped approximately 500,000 SNPs in 255 individuals (5 individuals from each of 51 worldwide populations) from the Human Genome Diversity Panel (HGDP-CEPH). When merged with non-overlapping SNPs typed previously in 250 of these same individuals, the resulting data consist of over 950,000 SNPs. We then analyzed the genetic relationships and ancestry of individuals without assigning them to populations, and we also identified candidate regions of recent positive selection at both the population and regional (continental) level. Our analyses both confirm and extend previous studies; in particular, we highlight the impact of various dispersals, and the role of substructure in Africa, on human genetic diversity. We also identified several novel candidate regions for recent positive selection, and a gene ontology (GO) analysis identified several GO groups that were significantly enriched for such candidate genes, including immunity and defense related genes, sensory perception genes, membrane proteins, signal receptors, lipid binding/metabolism genes, and genes involved in the nervous system. Among the novel candidate genes identified are two genes involved in the thyroid hormone pathway that show signals of selection in African Pygmies that may be related to their short stature.

Extrapair Paternity and Maternity in the Three-Toed Woodpecker, Picoides tridactylus: Insights from Microsatellite-Based Parentage Analysis:

Molecular techniques have revealed that avian mating systems are more diverse and complex than previously thought. We used microsatellite markers to determine genetic parentage, the prevalence of extrapair paternity and quasi-parasitism (i.e. situations where a male's extrapair mate lay in his nest) in a socially monogamous population of three-toed woodpeckers (Picoides tridactylus) in southern Finland. A total of 129 adults and nestlings, representing 5-9 families annually from 2004-2007, were genotyped at up to ten microsatellite loci. The results of genetic assignment tests confirmed that monogamous parentage characterized the majority (84.6%, 22/26) of broods, and that most (93.8%, 75/80) nestlings were the offspring of their social parents. Two of 80 nestlings (2.5%) in two of 26 broods (7.7%) were sired by extrapair males and quasi-parasitism occurred in 3.8% (3/80) of nestlings and 7.7% (2/26) of broods. Hence, the levels of extrapair parentage were low, possibly because both genetic polygyny and polyandry are constrained by the high paternal effort required for parental care. The co-occurrence of low levels of extrapair paternity and quasi-parasitism are discussed in light of ecological and behavioural factors characterizing the species biology.

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Clock Quotes

Wed, 18 Nov 2009 03:56:22 -0500

It is easy to fly into a passion - anybody can do that - but to be angry with the right person to the right extent and at the right time and with the right object and in the right way - that is not easy, and it is not everyone who can do it.

- Aristotle

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NESCent Travel Award - only two weeks left to submit your entries!

Tue, 17 Nov 2009 22:31:51 -0500

The application deadline for the NESCent blogging competition and travel award to ScienceOnline2010 is December 1, 2009. So hurry up - see the contest conditions and entries so far and meet the judges.

So, hurry up. Write (or choose an existing) post in the area of evolutionary biology and send it in. Two lucky winners will get travel grants to ScienceOnline2010. Yes, we are full, and there are 85 people on the waiting list. But the two NESCent winners have their spots saved just for them!

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The Open Laboratory 2009 - the deadline is looming!

Tue, 17 Nov 2009 17:09:56 -0500

Reminder: Deadline is December 1st at midnight EST!

Here are the submissions for OpenLab 2009 to date (under the fold). You can buy the 2006, 2007 and 2008 editions at Lulu.com. Please use the submission form to add more of your and other people's posts (remember that we are looking for original poems, art, cartoons and comics, as well as essays):

Make sure that the submitted posts are possible (and relatively easy) to convert into print. Posts that rely too much on video, audio, color photographs, copyrighted images, or multitudes of links just won't do.

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