Monthly Archives: September 2009

The Best of September

I have posted 131 times in September (exact same number as August), including many cool videos as well as a few pictures from a recent trip to the zoo. This month I also started importing the best links I posted on Twitter over the day, in Tweetlinks.
In September I interviewed Victor Henning, John Wilbanks and Kevin Emamy.
At work, the most exciting news was the release of Article-Level Metrics at PLoS – Download Data. I announced the Blog Pick Of The Month and that PLoS ONE won the ’09 ALPSP Award for Publishing Innovation!. Then I did an Interview with Dr.Derya Unutmaz, Section Editor for Immunology at PLoS ONE and told you about our cool new dinosaur paper.
Speaking of dinosarus, it was also the time to announce the Open Dinosaur Project.
I got a brand new Homepage and did some fiddling around with my About Me page here.
I got on the editorial board of the Journal of Science Communication.
I made the first big ScienceOnline2010 update, went on the radio to talk about it and announced a new sponsor and travel grants.
The best post of the month was Talkin’ Trash about the reporting from the Northern Pacific Gyre., a new science news service was anounced, with mixed reactions from the twitterverse, which prompted me to ask what investigative science reporting is.
This month was also an important date in my life.
I went to Techie Tuesday and The Long Table and next is a concert by Leonard Cohen.


Tweetlinks, 9-30-09

Follow me on Twitter to get these, and more, in something closer to Real Time:
Interplanetary paleontology?
Policy change before peer review: OA needed?
A Sick T. rex
Peter Lawrence’s Kafta tale of research grant funding
Ensuring Integrity in Comparative Effectiveness Research: Accentuate the Negative
Obama announces $5 bln for new medical research
Conference travel fellowship for best evolution-themed blog in 2009
Write a blogpost about evolution, compete, get famous and win a ticket to an interesting conference!
The Neural Correlates of Religious and Nonreligious Belief
Coming to Twitter: Create Sharable Lists of Users

Conference travel fellowship for best evolution‐themed blog in 2009

We are very excited to announce a new sponsor for ScienceOnline2010! It is National Evolutionary Synthesis Center (NESCent). Among some other ways they will help the meeting get bigger and better than ever, the good folks at NESCent are also going to help two bloggers with travel costs to the conference. Read carefully how you can get one of these two grants:

Application deadline: December 1, 2009   
Are you a blogger who is interested in evolution? The National Evolutionary Synthesis Center (NESCent) is offering two travel awards to attend ScienceOnline2010, a science communication 
conference to be held January 14‐17th, 2010, in North Carolina’s Research Triangle Park. 
The awards offer the opportunity to travel to North Carolina to meet with several hundred 
writers, editors, scientists and educators to explore how online tools are changing the way 
science is done and communicated to the public. Each winner will receive $750 to cover 
travel, lodging, and other expenses to attend the conference. In addition, winners are 
invited to spend the morning of Friday January 15th interacting with scientists at NESCent, 
and to attend a lunch in their honor. For more information about ScienceOnline2010, visit:
To apply for an award, writers should submit a blog post that highlights current or emerging
evolutionary research. In order to be valid, posts must deal with scientific results appearing
in 2009. Posts should be 750‐1500 words, and must mention the NESCent contest.
Two recipients will be chosen by a panel of judges from both NESCent and the science 
blogging community.
Please send your name, contact information, the title and date of your blog post, and a 
URL to 
Winners will be notified by December 15th, 2009.  
The purpose of this contest is to encourage the best of evolutionary writing on the Web.
The awards are sponsored by the National Evolutionary Synthesis Center an NSF‐funded 
research center operated by Duke University, North Carolina State University and the 
University of North Carolina at Chapel Hill. Known by its acronym NESCent, the center’s 
goal is to promote collaborative, cross-disciplinary research in evolutionary biology. 
For more information about the center, visit
Contact either of the program managers for more information about the contest: 
Robin Smith  
Phone: 919‐668‐4544 Email: 
Craig McClain  
Phone: 919‐668‐4590 
National Evolutionary Synthesis Center (NESCent) 
2024 W. Main Street, Suite A200 Durham, NC 27705 
NESCent logos are available for download at:

Nescent logo.png

Clock Quotes

Ogden’s Law: The sooner you get behind, the more time you will have to catch up.
– Alan R. Ogden

Tweetlinks, 9-29-09

Follow me on Twitter to get these, and more, in something closer to Real Time:
The Imaginary Journal of Poetic Economics: PLoS article-level metrics: substantial value add for authors
Is ‘Good Enough’ Good Enough for You?
Almost time for PLoS ONE Blog Pick Of The Month: Hurry up!
This is actually kind of serious: ‘Real Lives and White Lies in the Funding of Scientific Research’
How to provide safe, quality hospital care by increasing transparency
Adventures in Academia: On open access, Stanford’s leadership falters
Mark Patterson’s (PLoS) talk ‘Re-Engineering the Scientific Journal’ from the 1st OASPA Conference
The ABC of PLoS ONE – from ‘ant’ to ‘zebu’, we cover it all.
Triangle emerges as hotbed of advanced analytics
Take a Stand: How journalism can regain its relevance
Was Mighty T. Rex ‘Sue’ Felled By A Lowly Parasite?
Electric Fish Turn Down Charge for Energy Efficiency
Truth-seeking professionals and the public: Why is journalism unique? – why are academics/scientists given freedom, but journalists asked to relinquish it?
New Zealand launches a Science blog network! SciBlogs. Here is the press release: NZ’s largest science blog network goes live (Daniel Collins and Fabiana Kubke are familiar names to me – how about you?)
Last day to vote for @GrrlScientist – Who will go to Antarctica to be your official blogger?
Building Blogs of Science: On the virtues of having a lap
Next Generation Science: ScienceOnline2010 – Conference on Science and the Web

New and Exciting in PLoS ONE

There are 32 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:
Common Avian Infection Plagued the Tyrant Dinosaurs:

Tyrannosaurus rex and other tyrannosaurid fossils often display multiple, smooth-edged full-thickness erosive lesions on the mandible, either unilaterally or bilaterally. The cause of these lesions in the Tyrannosaurus rex specimen FMNH PR2081 (known informally by the name ‘Sue’) has previously been attributed to actinomycosis, a bacterial bone infection, or bite wounds from other tyrannosaurids. We conducted an extensive survey of tyrannosaurid specimens and identified ten individuals with full-thickness erosive lesions. These lesions were described, measured and photographed for comparison with one another. We also conducted an extensive survey of related archosaurs for similar lesions. We show here that these lesions are consistent with those caused by an avian parasitic infection called trichomonosis, which causes similar abnormalities on the mandible of modern birds, in particular raptors. This finding represents the first evidence for the ancient evolutionary origin of an avian transmissible disease in non-avian theropod dinosaurs. It also provides a valuable insight into the palaeobiology of these now extinct animals. Based on the frequency with which these lesions occur, we hypothesize that tyrannosaurids were commonly infected by a Trichomonas gallinae-like protozoan. For tyrannosaurid populations, the only non-avian dinosaur group that show trichomonosis-type lesions, it is likely that the disease became endemic and spread as a result of antagonistic intraspecific behavior, consumption of prey infected by a Trichomonas gallinae-like protozoan and possibly even cannibalism. The severity of trichomonosis-related lesions in specimens such as Tyrannosaurus rex FMNH PR2081 and Tyrannosaurus rex MOR 980, strongly suggests that these animals died as a direct result of this disease, mostly likely through starvation.

Dragon’s Paradise Lost: Palaeobiogeography, Evolution and Extinction of the Largest-Ever Terrestrial Lizards (Varanidae):

The largest living lizard species, Varanus komodoensis Ouwens 1912, is vulnerable to extinction, being restricted to a few isolated islands in eastern Indonesia, between Java and Australia, where it is the dominant terrestrial carnivore. Understanding how large-bodied varanids responded to past environmental change underpins long-term management of V. komodoensis populations. We reconstruct the palaeobiogeography of Neogene giant varanids and identify a new (unnamed) species from the island of Timor. Our data reject the long-held perception that V. komodoensis became a giant because of insular evolution or as a specialist hunter of pygmy Stegodon. Phyletic giantism, coupled with a westward dispersal from mainland Australia, provides the most parsimonious explanation for the palaeodistribution of V. komodoensis and the newly identified species of giant varanid from Timor. Pliocene giant varanid fossils from Australia are morphologically referable to V. komodoensis suggesting an ultimate origin for V. komodoensis on mainland Australia (>3.8 million years ago). Varanus komodoensis body size has remained stable over the last 900,000 years (ka) on Flores, a time marked by major faunal turnovers, extinction of the island’s megafauna, the arrival of early hominids by 880 ka, co-existence with Homo floresiensis, and the arrival of modern humans by 10 ka. Within the last 2000 years their populations have contracted severely. Giant varanids were once a ubiquitous part of Subcontinental Eurasian and Australasian faunas during the Neogene. Extinction played a pivotal role in the reduction of their ranges and diversity throughout the late Quaternary, leaving only V. komodoensis as an isolated long-term survivor. The events over the last two millennia now threaten its future survival.

The Origin and Initial Rise of Pelagic Cephalopods in the Ordovician:

During the Ordovician the global diversity increased dramatically at family, genus and species levels. Partially the diversification is explained by an increased nutrient, and phytoplankton availability in the open water. Cephalopods are among the top predators of todays open oceans. Their Ordovician occurrences, diversity evolution and abundance pattern potentially provides information on the evolution of the pelagic food chain. We reconstructed the cephalopod departure from originally exclusively neritic habitats into the pelagic zone by the compilation of occurrence data in offshore paleoenvironments from the Paleobiology Database, and from own data, by evidence of the functional morphology, and the taphonomy of selected cephalopod faunas. The occurrence data show, that cephalopod associations in offshore depositional settings and black shales are characterized by a specific composition, often dominated by orthocerids and lituitids. The siphuncle and conch form of these cephalopods indicate a dominant lifestyle as pelagic, vertical migrants. The frequency distribution of conch sizes and the pattern of epibionts indicate an autochthonous origin of the majority of orthocerid and lituitid shells. The consistent concentration of these cephalopods in deep subtidal sediments, starting from the middle Tremadocian indicates the occupation of the pelagic zone early in the Early Ordovician and a subsequent diversification which peaked during the Darriwilian. The exploitation of the pelagic realm started synchronously in several independent invertebrate clades during the latest Cambrian to Middle Ordovician. The initial rise and diversification of pelagic cephalopods during the Early and Middle Ordovician indicates the establishment of a pelagic food chain sustainable enough for the development of a diverse fauna of large predators. The earliest pelagic cephalopods were slowly swimming vertical migrants. The appearance and early diversification of pelagic cephalopods is interpreted as a consequence of the increased food availability in the open water since the latest Cambrian.

The Cultural Dynamics of Copycat Suicide:

The observation that suicides sometimes cluster in space and/or time has led to suggestions that these clusters are caused by the social learning of suicide-related behaviours, or “copycat suicides”. Point clusters are clusters of suicides localised in both time and space, and have been attributed to direct social learning from nearby individuals. Mass clusters are clusters of suicides localised in time but not space, and have been attributed to the dissemination of information concerning celebrity suicides via the mass media. Here, agent-based simulations, in combination with scan statistic methods for detecting clusters of rare events, were used to clarify the social learning processes underlying point and mass clusters. It was found that social learning between neighbouring agents did generate point clusters as predicted, although this effect was partially mimicked by homophily (individuals preferentially assorting with similar others). The one-to-many transmission dynamics characterised by the mass media were shown to generate mass clusters, but only where social learning was weak, perhaps due to prestige bias (only copying prestigious celebrities) and similarity bias (only copying similar models) acting to reduce the subset of available models. These findings can help to clarify and formalise existing hypotheses and to guide future empirical work relating to real-life copycat suicides.

Identification of Copy Number Variants Defining Genomic Differences among Major Human Groups:

Understanding the genetic contribution to phenotype variation of human groups is necessary to elucidate differences in disease predisposition and response to pharmaceutical treatments in different human populations. We have investigated the genome-wide profile of structural variation on pooled samples from the three populations studied in the HapMap project by comparative genome hybridization (CGH) in different array platforms. We have identified and experimentally validated 33 genomic loci that show significant copy number differences from one population to the other. Interestingly, we found an enrichment of genes related to environment adaptation (immune response, lipid metabolism and extracellular space) within these regions and the study of expression data revealed that more than half of the copy number variants (CNVs) translate into gene-expression differences among populations, suggesting that they could have functional consequences. In addition, the identification of single nucleotide polymorphisms (SNPs) that are in linkage disequilibrium with the copy number alleles allowed us to detect evidences of population differentiation and recent selection at the nucleotide variation level. Overall, our results provide a comprehensive view of relevant copy number changes that might play a role in phenotypic differences among major human populations, and generate a list of interesting candidates for future studies.

Continue reading

Today’s carnivals

Grand Rounds Vol. 6 No. 2 are up on Laika’s MedLibLog