Yearly Archives: 2007

Knowledge-Able Citizen

The other day, Kate organized a talk by Sheila Jasanoff about science communication and subsequently summarized the talk on her blog. You need to read the whole thing, but the main point is that there is a difference between a one-to-many communication of usual science communication (the ‘public service model’), including science education, policy speaches, etc., more often than not presented by non-scientists, e.g., journalists, politicians, etc. and the many-to-many interactive engaging of scientists with the public in a two-way communication (the ‘public sphere model’):

Thus, perhaps the issue is not how we package science, but how we engage the public to think critically about the science. While packaging can be done carefully and with reference to specific audiences, Jasanoff maintained that packaging fails to energize the ideals of the public, which would represent the most forward-thinking approach, and thus may represent apathy or acquiescence. Only after conveying the deeper importance of science will the public lend its energy and support to the scientific enterprise, as, in Jasanoff’s words, “all human-created work is worth reflecting on.”

In a follow-up post Kate elaborates on the idea from her own perspective:

But scientific literacy stems from much more than this initial info-bite. I have rarely had someone who, after I’ve spouted some sort of scientific semi-nonsense, hasn’t asked me insightful questions and pushed to understand more about it. Whether a scientist or non-scientist, most people have an innate curiousity that drives us to understand our surroundings, who we are, how we work – all the major fundamental questions driving science itself. When kids are little, this curiosity is wonderfully unaffected, but as we age, we either grow more jaded, more insecure, more over-scheduled, more whatever that causes us to restrict that curiosity, securing it away with an airtight cap. So, to me, Jasanoff’s argument on behalf of the Knowledge-Able Citizen rings true – society is composed of people very much capable of knowledge, of curiousity, and of understanding. And, if many of those are willing to engage with science, given the opportunity and the time, it seems that the most effective way to communicate science is by nurturing that curiosity, encouraging critical scientific thinking, and engaging the public more deeply in thought-provoking, challenging issues. The seeds of it are already there.

ClockQuotes

Sometimes a scream is better than a thesis.
– Ralph Waldo Emerson

My Picks from ScienceDaily

Tiny Crow Camera Spies On Clever Birds:

A new technique developed by Oxford University zoologists enables researchers to ‘hitch a ride’ with wild birds and witness their natural and undisturbed behaviour. The scientists developed miniaturised video cameras with integrated radio-tags that can be carried by wild, free-flying birds. Using this new ‘video-tracking’ technology, they spied on the behaviour of New Caledonian crows, a species renowned for its sophisticated use of tools, recording behaviours never seen before.

Diet With A Little Meat Uses Less Land Than Many Vegetarian Diets:

A low-fat vegetarian diet is very efficient in terms of how much land is needed to support it. But adding some dairy products and a limited amount of meat may actually increase this efficiency, Cornell researchers suggest.

Early Apes Walked Upright 15 Million Years Earlier Than Previously Thought, Evolutionary Biologist Argues:

An extraordinary advance in human origins research reveals evidence of the emergence of the upright human body plan over 15 million years earlier than most experts have believed. More dramatically, the study confirms preliminary evidence that many early hominoid apes were most likely upright bipedal walkers sharing the basic body form of modern humans.

Difference Between Fish And Humans: Century-old Developmental Question Answered:

Embryologists at UCL (University College London) have helped solve an evolutionary riddle that has been puzzling scientists for over a century. They have identified a key mechanism in the initial stages of an embryo’s development that helps differentiate more highly evolved species, including humans, from less evolved species, such as fish. The findings of the research, funded by the Biotechnology and Biological Sciences Research Council (BBSRC), were published online by the journal Nature.

Today’s Carnivals

Tangled Bank #90 is up on The Other 95%
International Carnival of Pozitivities #16 is up on Ogre’s Politics and Views
The 140th Carnival of Education is up on The Tempered Radical
Carnival of The Liberals #49 is up on Tangled Up in Blue Guy
Carnival of Homeschooling #93 is up on Apollos Academy

Science Blogging Conference – who is coming? (Blogging Science Librarians)

2008NCSBClogo200.pngThere are 100 days until the Science Blogging Conference. The wiki is looking good, the Program is shaping up nicely, and there is more and more blog and media coverage already. There are already 83 registered participants and if you do not register soon, it may be too late once you decide to do so (we’ll cap at about 230). Between now and the conference, I will be highlighting some of the people who will be there, for you to meet in person if you register in time.
books1.gifChristina Pikas is a science librarian at The Johns Hopkins University Applied Physics Laboratory. She blogs on Christina’s LIS Rant and she can tell you how wonderful last year’s conference was.
John Dupuis is the Head of the Steacie Science & Engineering Library at York University in Toronto and, as you know, he runs the wonderful blog Confessions of a Science Librarian.

ClockQuotes

There are times when one would like to hang the whole human race and finish the farce.
– Mark Twain

With Arctic Ice Gone, Walruses go South to Alaska’s Beaches

Melting Sea Ice Forcing Walruses Ashore:

Thousands of walrus have appeared on Alaska’s northwest coast in what conservationists are calling a dramatic consequence of global warming melting the Arctic sea ice.
Alaska’s walrus, especially breeding females, in summer and fall are usually found on the Arctic ice pack. But the lowest summer ice cap on record put sea ice far north of the outer continental shelf, the shallow, life-rich shelf of ocean bottom in the Bering and Chukchi seas.

[Via Russ Williams]

New and Exciting in PLoS ONE

As usual on Tuesday nights, lots of cool stuff got published on PLoS ONE today. Here are some of my picks, but you should check all 30 of them (so, this week I am correct – there are now 1000+ articles on PLoS ONE):
Large-Scale Mitochondrial DNA Analysis of the Domestic Goat Reveals Six Haplogroups with High Diversity:

Studying the genetic diversity of domesticated animals can provide insights into their domestication, and even the history of human migration. In this paper Pompanon and colleagues study mitochondrial DNA diversity of the domestic goat from 2430 animals from widespread Old World geographic origins. The researchers find a very high degree of mitochondrial diversity amongst goats, but suggest that even with such a large dataset, little can be concluded about the origin of goat domestication.

The Environmental Dependence of Inbreeding Depression in a Wild Bird Population:

Evolutionary genetic theory suggests that if related individuals breed, their offspring are likely to be less “fit” (or evolutionarily successful) than outbred offspring, because of the increased chance of inheriting two copies of a harmful recessive gene. The authors of this paper analysed the interaction between environment and inbreeding on individual fitness in a population of great tits. Their results suggest that in wild populations, the interaction between inbreeding and environment on fitness may be considerable.

Wnt and TGF-β Expression in the Sponge Amphimedon queenslandica and the Origin of Metazoan Embryonic Patterning:

The origin of metazoan development and differentiation was contingent upon the evolution of cell adhesion, communication and cooperation mechanisms. While components of many of the major cell signalling pathways have been identified in a range of sponges (phylum Porifera), their roles in development have not been investigated and remain largely unknown. Here, we take the first steps toward reconstructing the developmental signalling systems used in the last common ancestor to living sponges and eumetazoans by studying the expression of genes encoding Wnt and TGF-β signalling ligands during the embryonic development of a sponge.
Using resources generated in the recent sponge Amphimedon queenslandica (Demospongiae) genome project, we have recovered genes encoding Wnt and TGF-β signalling ligands that are critical in patterning metazoan embryos. Both genes are expressed from the earliest stages of Amphimedon embryonic development in highly dynamic patterns. At the time when the Amphimedon embryos begin to display anterior-posterior polarity, Wnt expression becomes localised to the posterior pole and this expression continues until the swimming larva stage. In contrast, TGF-β expression is highest at the anterior pole. As in complex animals, sponge Wnt and TGF-β expression patterns intersect later in development during the patterning of a sub-community of cells that form a simple tissue-like structure, the pigment ring. Throughout development, Wnt and TGF-β are expressed radially along the anterior-posterior axis.
We infer from the expression of Wnt and TGF-β in Amphimedon that the ancestor that gave rise to sponges, cnidarians and bilaterians had already evolved the capacity to direct the formation of relatively sophisticated body plans, with axes and tissues. The radially symmetrical expression patterns of Wnt and TGF-β along the anterior-posterior axis of sponge embryos and larvae suggest that these signalling pathways contributed to establishing axial polarity in the very first metazoans.

Maladaptation and the Paradox of Robustness in Evolution:

Organisms use a variety of mechanisms to protect themselves against perturbations. For example, repair mechanisms fix damage, feedback loops keep homeostatic systems at their setpoints, and biochemical filters distinguish signal from noise. Such buffering mechanisms are often discussed in terms of robustness, which may be measured by reduced sensitivity of performance to perturbations.
I use a mathematical model to analyze the evolutionary dynamics of robustness in order to understand aspects of organismal design by natural selection. I focus on two characters: one character performs an adaptive task; the other character buffers the performance of the first character against perturbations. Increased perturbations favor enhanced buffering and robustness, which in turn decreases sensitivity and reduces the intensity of natural selection on the adaptive character. Reduced selective pressure on the adaptive character often leads to a less costly, lower performance trait.
The paradox of robustness arises from evolutionary dynamics: enhanced robustness causes an evolutionary reduction in the adaptive performance of the target character, leading to a degree of maladaptation compared to what could be achieved by natural selection in the absence of robustness mechanisms. Over evolutionary time, buffering traits may become layered on top of each other, while the underlying adaptive traits become replaced by cheaper, lower performance components. The paradox of robustness has widespread implications for understanding organismal design.

Homeotic Evolution in the Mammalia: Diversification of Therian Axial Seriation and the Morphogenetic Basis of Human Origins:

Despite the rising interest in homeotic genes, little has been known about the course and pattern of evolution of homeotic traits across the mammalian radiation. An array of emerging and diversifying homeotic gradients revealed by this study appear to generate new body plans and drive evolution at a large scale.
This study identifies and evaluates a set of homeotic gradients across 250 extant and fossil mammalian species and their antecedents over a period of 220 million years. These traits are generally expressed as co-linear gradients along the body axis rather than as distinct segmental identities. Relative position or occurrence sequence vary independently and are subject to polarity reversal and mirroring. Five major gradient modification sets are identified: (1)-quantitative changes of primary segmental identity pattern that appeared at the origin of the tetrapods ; (2)-frame shift relation of costal and vertebral identity which diversifies from the time of amniote origins; (3)-duplication, mirroring, splitting and diversification of the neomorphic laminar process first commencing at the dawn of mammals; (4)-emergence of homologically variable lumbar lateral processes upon commencement of the radiation of therian mammals and ; (5)-inflexions and transpositions of the relative position of the horizontal septum of the body and the neuraxis at the emergence of various orders of therian mammals. Convergent functional changes under homeotic control include laminar articular engagement with septo-neural transposition and ventrally arrayed lumbar transverse process support systems.
Clusters of homeotic transformations mark the emergence point of mammals in the Triassic and the radiation of therians in the Cretaceous. A cluster of homeotic changes in the Miocene hominoid Morotopithecus that are still seen in humans supports establishment of a new “hominiform” clade and suggests a homeotic origin for the human upright body plan.

Nullomers: Really a Matter of Natural Selection?:

Nullomers are short DNA sequences that are absent from the genomes of humans and other species. Assuming that nullomers are the signatures of natural selection against deleterious sequences in humans, the use of nullomers in drug target identification, pesticide development, environmental monitoring, and forensic applications has been envisioned.
Here, we show that the hypermutability of CpG dinucleotides, rather than the natural selection against the nullomer sequences, is likely the reason for the phenomenal event of short sequence motifs becoming nullomers. Furthermore, many reported human nullomers differ by only one nucleotide, which reinforces the role of mutation in the evolution of the constellation of nullomers in populations and species. The known nullomers in chimpanzee, cow, dog, and mouse genomes show patterns that are consistent with those seen in humans.
The role of mutations, instead of selection, in generating nullomers cast doubt on the utility of nullomers in many envisioned applications, because of their dependence on the role of lethal selection on the origin of nullomers.

Demographic Histories of ERV-K in Humans, Chimpanzees and Rhesus Monkeys:

We detected 19 complete endogenous retroviruses of the K family in the genome of rhesus monkey (Macaca mulatta; RhERV-K) and 12 full length elements in the genome of the common chimpanzee (Pan troglodytes; CERV-K). These sequences were compared with 55 human HERV-K and 20 CERV-K reported previously, producing a total data set of 106 full-length ERV-K genomes. Overall, 61% of the human elements compared to 21% of the chimpanzee and 47% of rhesus elements had estimated integration times less than 4.5 million years before present (MYBP), with an average integration times of 7.8 MYBP, 13.4 MYBP and 10.3 MYBP for HERV-K, CERV-K and RhERV-K, respectively. By excluding those ERV-K sequences generated by chromosomal duplication, we used 63 of the 106 elements to compare the population dynamics of ERV-K among species. This analysis indicated that both HERV-K and RhERV-K had similar demographic histories, including markedly smaller effective population sizes, compared to CERV-K. We propose that these differing ERV-K dynamics reflect underlying differences in the evolutionary ecology of the host species, such that host ecology and demography represent important determinants of ERV-K dynamics.

SIRNA-Directed In Vivo Silencing of Androgen Receptor Inhibits the Growth of Castration-Resistant Prostate Carcinomas:

Prostate carcinomas are initially dependent on androgens, and castration or androgen antagonists inhibit their growth. After some time though, tumors become resistant and recur with a poor prognosis. The majority of resistant tumors still expresses a functional androgen receptor (AR), frequently amplified or mutated.
To test the hypothesis that AR is not only expressed, but is still a key therapeutic target in advanced carcinomas, we injected siRNA targeting AR into mice bearing exponentially growing castration-resistant tumors. Quantification of siRNA into tumors and mouse tissues demonstrated their efficient uptake. This uptake silenced AR in the prostate, testes and tumors. AR silencing in tumors strongly inhibited their growth, and importantly, also markedly repressed the VEGF production and angiogenesis.
Our results demonstrate that carcinomas resistant to hormonal manipulations still depend on the expression of the androgen receptor for their development in vivo. The siRNA-directed silencing of AR, which allows targeting overexpressed as well as mutated isoforms, triggers a strong antitumoral and antiangiogenic effect. siRNA-directed silencing of this key gene in advanced and resistant prostate tumors opens promising new therapeutic perspectives and tools.

Implementing Routine HIV Testing: The Role of State Law:

In September 2006, the Centers for Disease Control and Prevention (CDC) recommended routine HIV testing for all Americans aged 13-64, which would eliminate requirements for written consent and pretest counseling as previously required. However, this approach may conflict with state requirements concerning pretest counseling and informed consent for HIV testing. Our survey of state HIV testing laws demonstrates that the majority of states have HIV testing requirements that are inconsistent with the CDC’s recommendations. Moreover, states that have recently amended their laws have not eased the requirements for pretest counseling and informed consent. The reasons for the persistence of these legal requirements must be understood to effect policy changes to increase HIV testing.

Moderate Neonatal Stress Decreases Within-Group Variation in Behavioral, Immune and HPA Responses in Adult Mice:

The significance of behavioral neuroscience and the validity of its animal models of human pathology largely depend on the possibility to replicate a given finding across different laboratories. Under the present test and housing conditions, this axiom fails to resist the challenge of experimental validation. When several mouse strains are tested on highly standardized behavioral test batteries in different laboratories, significant strain×lab interactions are often detected. This limitation, predominantly due to elevated within-group variability observed in control subjects, increases the number of animals needed to address fine experimental questions. Laboratory rodents display abnormal stress and fear reactions to experimental testing, which might depend on the discrepancy between the stability of the neonatal environment and the challenging nature of the adult test and housing conditions.
Stimulating neonatal environments (e.g. brief maternal separations, increased foraging demands or maternal corticosterone supplementation) reduce stress and fear responses in adulthood. Here we tested whether reduced fearfulness associated with experimental testing would also reduce inter-individual variation. In line with our predictions, we show that a moderate elevation in neonatal corticosterone through maternal milk significantly reduces fear responses and inter-individual variability (average 44%) in adult mouse offspring.
We observed reduced variation in pain perception, novelty preference, hormonal stress response and resistance to pathogen infection. This suggests that the results of this study may apply to a relatively broad spectrum of neuro-behavioral domains. Present findings encourage a reconsideration of the basic principles of neonatal housing systems to improve the validity of experimental models and reduce the number of animals used.

Adaptive Evolution of a Stress Response Protein:

Some cancers are mediated by an interplay between tissue damage, pathogens and localised innate immune responses, but the mechanisms that underlie these linkages are only beginning to be unravelled.
Here we identify a strong signature of adaptive evolution on the DNA sequence of the mammalian stress response gene SEP53, a member of the epidermal differentiation complex fused-gene family known for its role in suppressing cancers. The SEP53 gene appears to have been subject to adaptive evolution of a type that is commonly (though not exclusively) associated with coevolutionary arms races. A similar pattern of molecular evolution was not evident in the p53 cancer-suppressing gene.
Our data thus raises the possibility that SEP53 is a component of the mucosal/epithelial innate immune response engaged in an ongoing interaction with a pathogen. Although the pathogenic stress mediating adaptive evolution of SEP53 is not known, there are a number of well-known candidates, in particular viruses with established links to carcinoma.

Habitat Fragmentation, Variable Edge Effects, and the Landscape-Divergence Hypothesis:

Edge effects are major drivers of change in many fragmented landscapes, but are often highly variable in space and time. Here we assess variability in edge effects altering Amazon forest dynamics, plant community composition, invading species, and carbon storage, in the world’s largest and longest-running experimental study of habitat fragmentation. Despite detailed knowledge of local landscape conditions, spatial variability in edge effects was only partially foreseeable: relatively predictable effects were caused by the differing proximity of plots to forest edge and varying matrix vegetation, but windstorms generated much random variability. Temporal variability in edge phenomena was also only partially predictable: forest dynamics varied somewhat with fragment age, but also fluctuated markedly over time, evidently because of sporadic droughts and windstorms. Given the acute sensitivity of habitat fragments to local landscape and weather dynamics, we predict that fragments within the same landscape will tend to converge in species composition, whereas those in different landscapes will diverge in composition. This ‘landscape-divergence hypothesis’, if generally valid, will have key implications for biodiversity-conservation strategies and for understanding the dynamics of fragmented ecosystems.

As always, look around, read the articles, rate them, post comments and annotations, send trackbacks if you blog about them, and if you want to do a Journal Club on one of them, let me know.

iPod wins the Nobel!

A newspaper should hire me to be that guy whose only job is to write titles and headlines. I can make them as misleading and sensationalist as the best of ’em!
But really, this year’s Nobel Prize for Physics is going to Albert Fert and Peter Grunberg for the invention of Giant Magnetoresistance. And yes, one of the many thingamajigs that uses this technology is iPod. But it makes for such a cool headline….

My Picks from ScienceDaily

Why Are Huge Numbers Of Camels Dying In Africa And Saudi Arabia?:

More than 2000 dromedaries — Arabian camels — have died since August 10 in Saudi Arabia. Various theories have been put forward to explain the numerous deaths. For several years, the Sahel and the Horn of Africa have also seen similar numbers of deaths. In 1995-1996, CIRAD worked on a fatal epizootic disease affecting dromedaries in Ethiopia.

Humans Unknowing Midwives For Pregnant Moose:

When it’s time for moose to give birth in the Greater Yellowstone Ecosystem, they head to where it is safest from predators — namely closer to people, according to a new study by the Wildlife Conservation Society. Published in the Royal Society’s journal Biology Letters, the study says that moose avoid predation of their calves by grizzly bears by moving closer to roads and other infrastructure prior to giving birth.

Ancient African Megadroughts May Have Driven Human Evolution — Out Of Africa:

From 135,000 to 90,000 years ago tropical Africa had megadroughts more extreme and widespread than any previously known for that region, according to new research.

Chronic Arguing With Your Spouse May Raise Your Heart Disease Risk:

Individuals whose close relationships have negative aspects, such as conflict and adverse exchanges, appear to have an increased risk of heart disease than those with more positive close relationships, according to a new report.

Meet Fred Gould (sans mosquitoes) over pizza

Another thing I will also have to miss – the Inaugural Event of the 2007-2008 Pizza Lunch Season of the Science Communicators of North Carolina (SCONC), on October 24th at Sigma Xi Center (the same place where we’ll have the Science Blogging Conference). Organized by The American Scientist and the Burroughs Wellcome Fund, the first Pizza Lunch Session will feature Dr.Fred Gould, professor of Entomology and Genetics at NCSU (whose Insect Ecology class blows one’s mind – one of the best courses I have ever taken in my life). Fred recently received The George Bugliarello Prize for an interdisciplinary article Genetic Strategies for Controlling Mosquito-Borne Diseases. You can read an article about him in Raleigh News and Observer or, even better, listen to him on this podcast on State Of Things a few weeks ago. Notice with what disdain he utters the term “junk DNA” – only once in the entire hour – in order to explain it (away).

Science Cafe Raleigh – Dinosaurs!

Darn – I’ll be out of town on that date, but you make sure to show up! The October meeting of Science Cafe Raleigh will be on the 23rd at my favourite Irish pub in Raleigh, Tir Na Nog, and the speaker is Dr. Mary Schweitzer, the NCSU researcher who discovered and analyzed soft tissues in fossilized bones of T.rex:

Dinosaurs: Rewriting the Rules of Fossilization
Tuesday, October 23, 2007
6:30-8:30 p.m. with discussion beginning at 7 p.m. followed by Q&A
Location: Tir Na Nog, 218 South Blount St., 833-7795
Speaker: Dr. Mary Schweitzer
Dr. Mary Schweitzer studies dinosaur bones, as many paleontologists do. But recently she has been rewriting the rules of fossilization with her research at the microscopic and molecular levels. Her most fascinating finds have included preserved soft tissues, such as collagen and what appear to be ancient blood vessels, inside a 68-million-year-old T. rex. Come discover how her research has confirmed many connections between dinosaurs and birds and astonished scientists who have long believed that soft tissues would never be found inside fossilized bone.
Mary Schweitzer is the Museum’s Curator of Vertebrate Paleontology and an Associate Professor of Paleontology at NC State University. Her discovery of soft tissue inside a Tyrannosaurus rex thigh bone was named the 6th most important science story of 2005 by Discover magazine. She received a PhD in Biology and a Secondary Education Teaching Certificate from Montana State University, and a Bachelor’s degree in Communicative Disorders from Utah State University.

Laboratory Web Site and Video Awards

You may remember, from several months ago, that Attila started a contest for the best designed lab web page.
Soon, the project became too big for a lone blogger to tackle. Especially after an article about this appeared on the online pages of Nature. So, as Attila announced today, the contest goes Big Time.
The Scientist is now hosting the official contest. Of course, Attila is one of the judges. Several web-pages have already been nominated and now it is your job to think of the best-designed, prettiest, most-functional and most up-to-date laboratory homepages and nominate them for the prize.
Also, spread the word about this.

Today’s Carnivals

Encephalon #33 is up on GNIF Brain Blogger
Grand Rounds Vol. 4, No. 3 are up on Nurse Ratched’s Place
Carnival of the Green #98 is up on Planet on a Plate

New and Exciting from PLoS Biology and Medicine

Genetic Dissection of Behavioural and Autonomic Effects of Δ9-Tetrahydrocannabinol in Mice and the accompanying editorial Understanding Cannabinoid Psychoactivity with Mouse Genetic Models:

The fact that cannabis is the most widely used illicit drug has motivated a great deal of research aimed at understanding how it produces its psychoactive effects. Here I use the term psychoactive to describe the mild euphoria, altered perceptions, sense of relaxation, and sociability that often, but not always, accompany recreational cannabis use. Despite the difficulties inherent in working with lipophilic cannabinoids such as Δ9-tetrahydrocannabinol (THC), which is the primary psychoactive component of cannabis, our understanding of the mechanism of action of these compounds at the cellular level has increased dramatically over the past 20 years. However, a complete understanding of how cannabis elicits its psychoactive effects would include an appreciation of its actions at the cellular and network level as well as an identification of the neural circuits perturbed. The cannabinoid field has now matured to the point where investigators can begin to relate the cellular mechanisms of THC action to the behavioral effects of cannabis.

HCV-HIV Coinfection: Simple Messages from a Complex Disease:

Hepatitis C virus (HCV) and HIV infection are both major global health problems, each with their own specific unsolved and difficult issues of prevention, pathogenesis, and therapy. For HIV, many of the clinical problems experienced are related to loss of immunological control over relatively commonly encountered pathogens. In most of these cases (e.g., cytomegalovirus [CMV], Pneumocystis jiroveci. human herpesvirus-8), normal immunological control is quite efficient, and these organisms behave as “opportunists.” HCV is slightly different, in that immunological control in normal HIV-uninfected individuals is often poor, and HCV infection alone can lead to the gradual evolution of end-stage liver disease in normal hosts. However, although a consensus is forming about the basic details of the immune responses associated with acute control of HCV monoinfection, the long-term relationships between immune responses, viral load, and most importantly, disease progression in those who are persistently infected are still poorly understood.

Genes vs./plus Environment

My former SciBling David Dobbs regularly posts on the SciAm Blog, usually bringing in guest contributors highlighting novel research in neuroscience. Today, he invited Charles Glatt to review an interesting study on the interaction between genes and environment in development of depression. David writes:

This week reviewer Charles Glatt reviews a study that takes this investigation a level deeper, examining how two different gene variants show their power — or not — depending on whether a child is abused, nurtured, or both. As Glatt describes, this study, despite its grim subject, suggests promising things about the power of nurture to magnify nature’s gifts or lift its burdens.

In the study, two candidate genes identified as potentially predisposing people to depression were checked in two different environments – a nurturing one and an abusive one. Charles concludes:

As with any behavioral genetic study, one must be careful not to overinterpret these findings, because virtually no study in behavioral genetics is consistently or completely replicated. Nonetheless, some additional points about this paper can help inform us on the nature-nurture debate. First, depression scores and categorical diagnoses of depression were significantly higher in children with a history of maltreatment versus controls even before any genetic analysis was factored in. In a similar vein, the highest average depression score of any genotype category in the unabused control children was lower than the average depression score for any genotype category in the maltreated children; genes alone weren’t likely to make the child depressed, but maltreatment alone could.
These findings suggest that, at least regarding these specific polymorphisms, nurture beats nature. This conclusion will come as a relief to believers in human free will. It also argues strongly for the identification of children at risk for maltreatment and strong actions to reverse the negative effects of this experience.

Read the whole thing for details.

Journal Clubs – think of the future!

The recent return of Journal Clubs on PLoS ONE has been quite a success so far. People are watching from outside and they like what they see.
The first Journal Club article, on microbial metagenomics, has already, in just one week, gathered 3 ratings, each accompanied with a short comment, one trackback (this will be the second) and 7 annotations and 4 discussions eliciting further 14 responses in the comment threads. The 12-comment-and-growing thread on the usefulness of the term ‘Prokaryote’ is quite exciting, showing that it is not so hard to comment on PLoS ONE after all, once you get over the initial reluctance. You should join in the conversation there right now!
If you encounter a technical problem, please contact the Webmaster so the glitch can be fixed promptly. For a brand-new software built in-house, TOPAZ is performing remarkably well, but glitches do sometimes happen. It is essential to report those to the Webmaster so the IT/Web team can fix them quickly and make the site better and better for all users as time goes on. Just like anything else in development, it needs feedback in order to improve over time. For the time being, I guess, compose in Notepad, WordPad or something similar before copying and pasting there. And thank you for your participation.
One thing to keep in mind is that a PLoS ONE article is not a blog post – the discussion is not over once the post goes off the front page. There is no such thing as going off the front page! The article is always there and the discussion can go on and on for years, reflecting the changes in understanding of the topic over longer periods of time.
Imagine if half a century ago there was Internet and there were Open Access journals with commenting capability like PLoS ONE. Now imagine if Watson and Crick published their paper on the DNA structure in such a journal. Now imagine logging in today and reading five decades of comments, ratings and annotations accumulated on the paper!!!! What a treasure-trove of information! You hire a new graduate student in molecular biology – or in history of science! – and the first assignment is to read all the commentary to that paper. There it is: all laid out – the complete history of molecular biology all in one spot, all the big names voicing their opinions, changing opinions over time, new papers getting published trackbacking back to the Watson-Crick paper and adding new information, debates flaring up and getting resolved, gossip now lost forever to history due to it being spoken at meetings, behind closed door or in hallways preserved forever for future students, historians and sociologists of science. What a fantastic resource to have!
Now imagine that every paper in history was like that (the first Darwin and Wallace letters to the Royal Society?!). Now realize that this is what you are doing by annotating PLoS ONE papers. It is not the matter so much of here-and-now as it is a contribution to a long-term assessment of the article, providing information to the future readers that you so wished someone left for you when you were reading other people’s papers in grad school and beyond. Which paper is good and which erroneous (and thus not to be, embarrassingly, cited approvingly) will not be a secret lab lore any more transmitted from advisor to student in the privacy of the office or lab, but out there for everyone to know. Every time you check out a paper that is new to you, you also get all the information on what others think about it. Isn’t that helpful, especially for students?
So, go forth and comment on papers in areas you are interested in. And if you are a member of a lab group, a graduate seminar, an honors class, or an AP Biology class, let me know if you would be interested in doing a Journal Club on one of the PLoS ONE papers in the future – a great exercise for you, nice exposure to your group, and a service to the scientific community of today and tomorrow.

DonorsChoose Update

The news came from high above that the Seed Media Group Science Literacy Grants program will match your donations up to $15,000. So, at this point in the fundraiser, every dollar you donate is worth two!
So, check out my challenge and check out my SciBlings’ challenges as well.
And yes, don’t forget the prizes! I just got a mug and a t-shirt yesterday and they look good!
ABATC%20coffee%20mug.jpg

Science Blogging Conference – who is coming? (Science Museums)

2008NCSBClogo200.pngThere are 101 days until the Science Blogging Conference. The wiki is looking good, the Program is shaping up nicely, and there is more and more blog and media coverage already. There are already many registered participants and if you do not register soon, it may be too late once you decide to do so (we’ll cap at about 230). Between now and the conference, I will be highlighting some of the people who will be there, for you to meet in person if you register in time.
mit_museum_logo.gifScience museums will be well represented at the Conference. So far, we know that John Durant, the Director of the MIT Museum, Troy Livingston, the Vice President for Innovation and Learning at the Museum of Life and Science in Durham, NC, and Roy Campbell, the Exhibit Director at North Carolina Museum of Natural Sciences in Raleigh, NC will be attending the proceedings.
Durham%20Museum%20Logo.jpg
NC%20museum%20logo.GIFIf you want to meet them in person, register today. Registration is free.

ClockQuotes

The curricula were unsophisticated, with a great deal of time wasted on penmanship and geography in the early grades and repetitions of the trivial history of New York City in higher grades.
– Martin Lewis Perl

Web

Some good, thought-provoking reads about the Web, social networking, publishing and blogging:
Aggregating scientific activity
Social Networks at Work Promise Bottom-Line Results
Would limiting career publication number revamp scientific publishing?
The Public Library of Science group
The Seven Principles of Community Building

My Picks from ScienceDaily

Genes From The Father Facilitate The Formation Of New Species:

The two closely related bird species, the collared flycatcher and the pied flycatcher, can reproduce with each other, but the females are more strongly attracted to a male of their own species. This has been shown by an international research team directed by Anna Qvarnström at Uppsala University and published in Science. They demonstrate that the gene for this sexual preference is found on the sex chromosome that is inherited from the father and that only females have a copy of. The discovery sheds new light on how new species are formed.

Primitive Plants Use Heat And Odor To Woo Pollinating Insects:

University of Utah scientists discovered a strange method of reproduction in primitive plants named cycads: The plants heat up and emit a toxic odor to drive pollen-covered insects out of male cycad cones, and then use a milder odor to draw the bugs into female cones so the plants are pollinated.

When Taking A Long Time Is Seen As A Good Thing:

Consumers often use the length of time a service takes as a measure of its quality. The longer a session lasts, the better the value. Indeed, a new study shows that this holds true even when judging something primarily by its duration can backfire — for example when a longer exercise program is actually less effective than a shorter regimen or for a lock-picking service.

Brain Images Make Cognitive Research More Believable:

People are more likely to believe findings from a neuroscience study when the report is paired with a colored image of a brain as opposed to other representational images of data such as bar graphs, according to a new Colorado State University study.

New Insights Into The Evolution Of The Human Genome:

Which came first, the chicken genome or the egg genome? Researchers have answered a similarly vexing (and far more relevant) genomic question: Which of the thousands of long stretches of repeated DNA in the human genome came first? And which are the duplicates?

Elephants’ Fear Of Angry Bees Could Help To Protect Them:

At a time when encroaching human development in former wildlife areas has compressed African elephants into ever smaller home ranges and increased levels of human-elephant conflict, a study in Current Biology, suggests that strategically placed beehives might offer a low-tech elephant deterrent and conservation measure.

Malaria Research Booming, But Scientific And Technical Gaps Apparent, Report Shows:

Malaria drug and vaccine research is booming. According to a new report launched in the UK by Australian researchers at The George Institute for International Health, 16 new malaria vaccine candidates are now in clinical trials; six new malaria drugs are about to reach the market; and by 2011 we will have up to 12 new anti-malarial drug product registered. However, this unprecedented level of malaria R&D activity is not necessarily all good news. The report’s authors found that the high number of malaria vaccine candidates was the result of scientific and technical gaps and lacking policy coordination rather than a reflection of cohesive global activity. Lack of coordination and planning mean that invested funding and efforts are not delivering as much as they should, and may be costing donors tens of millions of dollars.

How Do Cells Sense And Respond To Messages? Major Signal Transduction Discovery Made:

The chemical process known as acetylation plays a central role in cytokine receptor signal transduction – a fundamental biochemical cascade inside cells that controls the activity of antiviral and tumor-suppressing genes.

In Birds, Expecting To Mate Leads To Higher Fertilization Rates:

From an evolutionary perspective, the primary task of an organism is to pass along its genes to future generations. Such genetic transmission is usually assumed to be instinctive. However, a new study shows that species also learn to adapt to their surroundings in order to increase their “reproductive fitness”– the likelihood that they will successfully reproduce.

For Honey Bee Queens, Multiple Mating Makes Her Attractive To Workers:

The success of the “reign” of a honey bee queen appears to be determined to a large degree by the number of times she mates with drone bees.That is what research by scientists in the Department of Entomology and W.M. Keck Center for Behavioral Biology at North Carolina State University suggests. Dr. Freddie-Jeanne Richard, a post-doctoral research associate; Dr. David Tarpy, assistant professor and North Carolina Cooperative Extension apiculturist; and Dr. Christina Grozinger, assistant professor of insect genomics, found that the number of times a honey bee queen mates is a key factor in determining how attractive the queen is to the worker bees of a hive.

Say Hello to the newest Scibling!

This is really suspicious – magic perhaps! Every time I make a wish (and whisper it in prayer to the, hushhhhh, super-secret gods of atheists) for a favourite blog to get invited to join Scienceblogs.com, that actually happens in a matter of a few days. Poof! Just like that. Just look at today – Brian Switek just moved his lovely Laelaps blog from the old site to the new place right here.
Dinosaurs. Lots of dinosaurs! And much other good stuff – evolution, history of science, book reviews, cool animals… He’ll move his old legendary posts over to the new place gradually over time, so you should check the archives of his old site to get a glimpse, but for now, go to the new place and say Hello!

The Blogging Scholarship

You may remember last year’s contest, when my SciBling Shelley Batts was a Runner-up for the big prize.
The finalists for this year’s $10,000 scholarship have just been announced and Shelley is one of the finalists again. Hopefully, this year she’ll win.
And you can help her by voting for her.

DonorsChoose Update

The first week of the DonorsChoose fund-drive is up and the donations are coming in rapidly to a variety of school projects via my SciBlings’ challenges.
You can check out all the projects picked by my SciBlings here and my own here.
You can get to my pledge also by clicking on the thermometer on my sidebar (scroll down a little bit) and watch how the mercury in all of our thermometers rise over time. As you can see, 37% of my challenge has already been funded!
<!– –>


Thank you so much! If you continue being so fast and generous and we reach our goal too soon, I will add more projects to the pledge. Remember, the drive lasts the entire month of October.
And now, let me introduce some special “bribes” for you. I have placed my beautiful banner (with the permission of the artist) on some merchandise on Cafe Press. There are coffee mugs, a wall clock (how appropriate!) and several styles of t-shirts. Send me your receipts from DonorsChoose to be eligible for prizes. One item of your choice will be sent to the following people (who, with their permission, will be announced here on November 1st):
– the reader who donates a single, one-time, largest donation to my challenge.
– the reader who donates the largest total amount over the month of October to my challenge.
– the reader who gives the largest number of times during October to my challenge.
– the reader who donates through the challenges of the largest number of my SciBlings (including mine).
So, if you want a mug, a clock or a t-shirt (or in your e-mail, if you are a winner, you can ask for something else that can be had at Cafe Press, e.g., baseball hat, baby bib, or, gasp, underwear!), pick your preferred strategy and get started. If you have already donated over the past week, you are still eligible. Thank you in advance!

A Challenger to Elizabeth Dole?

Kirk Ross in this week’s ‘Carrboro Citizen’:

Jim Neal, a key Democratic Party fundraiser, is on the verge of announcing a run for U.S. Senate, sources close to Neal say.
Neal, a native of Greensboro who now lives in Chapel Hill, will head to Asheville this weekend for the Vance-Aycock Dinner, a traditional gathering of Democratic Party movers and shakers and a place where potential candidates often test the waters. He is expected to file official paperwork as early as this week.
Neal was a top fundraiser for the John Kerry and John Edwards ticket in 2004 and a major supporter of Gen. Wesley Clark’s bid for the Democratic nomination that year.
He is a former investment banker and is currently a financial advisor.
Dole, a one-term incumbent who has already announced for re-election, has been raising money in preparation for the race. A recent Elon Poll found that 53 percent of respondents indicated they are satisfied or very satisfied with the senator’s representation of North Carolina and 24 percent disapproved or strongly disapproved.
But both Democratic and Republican election handicappers say Dole is vulnerable because of her support of President Bush’s Iraq policies. The same poll shows that only 32 percent of North Carolinians polled approved of her job performance on Iraq and 78 percent — the highest percentage — said the war will influence their vote in 2008.

Sounds like a party insider with money and connections. Not a very familiar name, though. We’ll wait and see.

Science Blogging Conference – who is coming? (Open Access)

2008NCSBClogo200.pngThere are 102 days until the Science Blogging Conference. The wiki is looking good, the Program (now completely reshuffled) is shaping up nicely, and there is more and more blog and media coverage already. There are already 82 registered participants and if you do not register soon, it may be too late once you decide to do so (we’ll cap at about 230). Between now and the conference, I will be highlighting some of the people who will be there, for you to meet in person if you register in time.
Hemai%202.jpgHemai Parthasarathy is a dear friend of mine, and one of the Biggest Stars we managed to attract to our conference. After getting degrees in biophysics and systems neuroscience and some postdoc time in neuroscience, she decided to change her career trajectory and accepted the invitation from Nature to serve as an editor, where she remained for five years, and then joined the team that founded PLoS Biology where she worked as the Managing Editor for another 4.5 years. She has talked and written quite a lot about Open Access and the business of science publishing and you can hear her talking about it in this podcast recorded at the last SXSW conference.
At the Conference, she will lead the session on Open Science and you are invited to add questions, comments and ideas for the session by editing this wiki page. To meet Hemai in person, you’ll have to register for the conference – registration is free!

UNC researcher wins a Nobel for the Knock-Out Mouse

Dr. Oliver Smithies, the Excellence Professor of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, NC, USA, together with Mario R. Capecchi and Martin J. Evans, won this year’s Nobel Prize in Physiology and Medicine:

This year’s Nobel Laureates have made a series of ground-breaking discoveries concerning embryonic stem cells and DNA recombination in mammals. Their discoveries led to the creation of an immensely powerful technology referred to as gene targeting in mice. It is now being applied to virtually all areas of biomedicine – from basic research to the development of new therapies.
Gene targeting is often used to inactivate single genes. Such gene “knockout” experiments have elucidated the roles of numerous genes in embryonic development, adult physiology, aging and disease. To date, more than ten thousand mouse genes (approximately half of the genes in the mammalian genome) have been knocked out. Ongoing international efforts will make “knockout mice” for all genes available within the near future.

Update: Here is the UNC press release.
[Hat-tip to Abel]

ClockQuotes

Regret for the things we did can be tempered by time; it is regret for the things we did not do that is inconsolable.
– Sydney J. Harris

New on….

Chris Clarke explains eloquently what is, essentially, my blog commenting policy (though I transgress on other people’s blogs…sorry).
The Senate vote on the mandatory free access to NIH-funded research has been postponed, which gives you all a few more days to do your part!
John Dupuis interviews Richard Akerman. I met Richard at Scifoo, and John is coming to SBC. Both are science bloggers interested in new technologies and how they impact science libraries, so the interview is quite enlightening.
Dicyemida: Leading a double life – an invertebrate you probably never heard of, but if you love Cephalopods you should get worried….
Friday Ark #159 is up on The Modulator and Steve has picthed the Animeme to just the right audience for it. More and more posts are sprouting around the Web responding to the meme.
How to use Facebook as part of your business strategy – an excellent article by Steve Outing.
Waaay coool: Eigenfactor: Ranking and mapping scientific knowledge
Medical Student Bloggers, Best Medical Blogs and another list of Best Medical Blogs.
Evo-devo of mammalian molars – PZ Myers in his finest science blogging style (but read the preamble first).
Council of Europe accepts resolution opposing the teaching of creationism as a scientific discipline – read PvM and Archy.
Development of assymetry in the nervous system.
Spandrels: here, here and here.
RPM of evolgen is posting original, previously unpublished data on his blog. See the entire series (so far) here, here, here, here, here and here.

My Picks from ScienceDaily

Chimpanzees, Unlike Humans, Apply Economic Principles To Ultimatum Game:

New research from the Max Planck Institute of Evolutionary Anthropology in Leipzig, Germany shows that unlike humans, chimpanzees conform to traditional economic models. The research used a modification of one of the most widely used and accepted economic tools, the ultimatum game.

New Telomere Discovery Could Help Explain Why Cancer Cells Never Stop Dividing:

A group working at the Swiss Institute for Experimental Cancer Research (ISREC) in collaboration with the University of Pavia has discovered that telomeres, the repeated DNA-protein complexes at the end of chromosomes that progressively shorten every time a cell divides, also contain RNA.

Key Step Bird Flu Virus Takes To Spread Readily In Humans Identified:

Since it first appeared in Hong Kong in 1997, the H5N1 avian flu virus has been slowly evolving into a pathogen better equipped to infect humans. The final form of the virus, biomedical researchers fear, will be a highly pathogenic strain of influenza that spreads easily among humans.

Why Emotionally Charged Events Are So Memorable:

Both extensive psychological research and personal experiences confirm that events that happen during heightened states of emotion such as fear, anger and joy are far more memorable than less dramatic occurrences.

Negativity Is Contagious, Study Finds:

Though we may not care to admit it, what other people think about something can affect what we think about it. This is how critics become influential and why our parents’ opinions about our life choices continue to matter, long after we’ve moved out. But what kind of opinions have the most effect” An important new study in the Journal of Consumer Research reveals that negative opinions cause the greatest attitude shifts, not just from good to bad, but also from bad to worse.

Simplest Circadian Clocks Operate Via Orderly Phosphate Transfers:

Researchers at Harvard University and the Howard Hughes Medical Institute have found that a simple circadian clock found in some bacteria operates by the rhythmic addition and subtraction of phosphate groups at two key locations on a single protein. This phosphate pattern is influenced by two other proteins, driving phosphorylation to oscillate according to a remarkably accurate 24-hour cycle.

Related: A Circadian Clock that works in a test-tube explained and Bacteria do it differently

Science Blogging Conference – who is coming? (SciBlings)

2008NCSBClogo200.pngThere are 103 days until the Science Blogging Conference. The wiki is looking good, the Program is shaping up nicely, and there is more and more blog and media coverage already. There are already many registered participants and if you do not register soon, it may be too late once you decide to do so (we’ll cap at about 230). Here are some of the people who will be there, for you to meet in person if you register in time.
Zuska%27s%20headshot.jpgMy Scibling and dear friend, Suzanne Franks, aka Zuska describes herself as…well, go and read how she describes herself. If you write something sexist, Super-Zuska will put her cape on, fly to wherever in the world you are, and puke on your shoes. And if you donate to schools through Zuska’s Challenge on DonorsChoose, you will be eligible to win the Grand Prize: a t-shirt emblazoned with the unforgettable words: “Zuska says: Don’t make me puke on your shoes.”

Karen%27s%20headshot.JPGKaren Ventii, besides being a SciBling, is a Ph.D. student of biochemistry at Emory University in Atlanta GA and is looking for a career in science journalism or writing. Karen and Zuska will co-moderate a session on Gender and Race in science: online and offline. You can already start asking questions (by editing that wiki page).

ClockQuotes

For historians ought to be precise, truthful, and quite unprejudiced, and neither interest nor fear, hatred nor affection, should cause them to swerve from the path of truth, whose mother is history, the rival of time, the depository of great actions, the witness of what is past, the example and instruction of the present, the monitor of the future.
– Miguel de Cervantes

Dinosaurs are coming to Raleigh!

OK, I live here, yet I had to learn from Brian that the AMNH dinosaur exhibit is coming to the North Carolina Museum of Natural Sciences in downtown Raleigh. The exhibit will be open from October 26, 2007 till March 2, 2008 and I will make sure to go and see it while it is in town (and take pictures if they’ll let me and then blog about it). If you come from out of town to see the exhibit, don’t forget to also see the dinos that are on permanent display at the Museum: the Acrocanthosaurus (the only skeleton of its kind displayed anywhere – and it is not a cast either but the real thing) and Thescelosaurus ‘Willo’, the dinosaur with a heart.

Science 2.0 at SILS

Jeffrey Pomerantz invited me to give a brownbag lunch presentation on Science 2.0 yesterday at noon at the School of Information and Library Science at University of North Carolina at Chapel Hill. It was fun for me and I hope it was fun for the others in the room, about 20 or so of faculty and students in the School.
This was my first attempt at putting together such a presentation, something I will be called on to do several times over the next couple of months and more. I was happy I made it within one hour, excellent questions included, though I probably talked too long about blogs and too little on science video (and barely mentioned Second Life). I’ll be working on it in the future. Here are the links I used during the presentation (they will probably give you a pretty good idea what I was talking about):
My old posts about science blogging and Science 2.0:
Science Blogging – what it can be?
PLoS 500
Science 2.0
Nature Precedings
Where and how to find science blogs:
some science blogs and carnivals
An example of a carnival homepage
Last year’s Conference blog/media coverage
Blog collectives;
Scienceblogs.com
Nature Blog Network
Example of a successful/popular science blog:
Pharyngula
Examples of classroom science blogs:
Developmental Biology at UMM
BIO101 at NCWC
An example of Open Notebook Science:
Useful Chemistry Blog
Useful Chemistry Wiki
A Masters Thesis on a wiki
‘Nature’ experiments in Science 2.0:
Postgenomic
Connotea
Scintilla
Pre-peer-review pre-publishing:
Nature Precedings
Science on Facebook:
a post with a good collection of examples
PLoS group
Science on Second Life:
Drexel Island
Scifoo Lives On
Second Life Molecules
Science Social Networks:
Knowble
JeffsBench
Erudix
MyExperiment
Science video sites:
SciVee
JoVE
SciTalks
LabAction
Bioscreencast
DNATube
ScienceHack
FreeScienceLectures
Open Access Publishing:
Directory of Open Access Journals
Definition of Open Access
Open Access Resources
Public Library of Science

Could TRIPS save lives in Third World Countries by opening research articles?

That is one very interesting idea! This provision is usually used for getting medicines to 3rd world countries in times of emergency. So, why not research papers if the emergency warrants it? Gavin writes:

Imagine a scenario in which a developing country is facing a national health emergency, and there’s a research article that contains information that is highly relevant to addressing that emergency. Let’s say the emergency is an alarmingly high rate of mother-to-child transmission of HIV, and a new study shows a major breakthrough in preventing such transmission. And let’s say that unfortunately the article copyright is owned by the publisher (not the author), and the article is locked away behind a typical subscription barrier (usually around $30 per person to view it).
Could the government, asked Shahram, invoke TRIPs [The Agreement on Trade Related Aspects of Intellectual Property Rights] to simply bypass the copyright holder and disseminate the article across the nation?

Tell Gavin what you think.

Science Blogging Conference – who is coming? (Organizers)

2008NCSBClogo200.pngThere are 104 days until the Science Blogging Conference. The wiki is looking good, the Program is shaping up nicely, and there is more and more blog and media coverage already. There are already 81 registered participants and if you do not register soon, it may be too late once you decide to do so(we’ll cap at about 230). Starting today, I’ll start introducing the participants here, pretty much daily. I’ll start by getting the organizers out of the way first 😉

Anton.jpgAnton Zuiker is a blogger and a journalist, and currently works as manager of internal communications at Duke Medicine. He is the founder of BlogTogether and the driving force behind the local blogging community – no meetups, bloggercons or other events would have happened without him. Not to mention such initiatives as Storyblogging and Foodblogging. Read a nice recent story about Anton in the Raleigh News & Observer.

Blogger%20BBQ%20005.jpgBrian Russell is an independent Social Software and Multimedia Consultant and the local podcast and multimedia guru. A couple of years ago, he organized a Podcastercon about which I wrote this post. With his wife Ruby and a few other local political activists, he also writes Orange Politics, the popular hub of the local political scene (if you don’t show up there, you cannot win a local election, pretty much). Also, as far as I know, Brian and Ruby were the fist couple ever to use a blog to get their friends, in the comments, to suggest details about their wedding, from location and decorations, to the menu and her dress.

Blogger%20BBQ%20010.jpgPaul Jones is a blogger, a poet, a Blooker Prize judge, the director (and founder?) of Ibiblio.org and a professor at UNC schools of Journalism, where he teaches classes on topics like Blogging, We the Media and Virtual Communities. And again, being online is ‘in the family’ – as his wife Sally Greene (Go Greene!) is a member of the City Council who blogs beautifully.

Oh, and I’ll be there, too:
bora.JPG

So, if you want to meet us in person, you need to register – it’s free!

IgNobels announced!

The folks at the Journal of Improbable Research have announced this years winners!
This is the first time I have ever blogged about a study before it won an IgNobel!
So cool!

ClockQuotes

Life is a waste of time, time is a waste of life, so get wasted all of the time and have the time of your life.
– Michelle Mastrolacasa

New and Exciting in PLoS Community Journals

As always on Friday, there are new article published in the community journals – PLoS Pathogens, PLoS Computational Biology and PLoS Genetics. Here are few of my picks:
Growth of H5N1 Influenza A Viruses in the Upper Respiratory Tracts of Mice
A Single Mutation in the PB1-F2 of H5N1 (HK/97) and 1918 Influenza A Viruses Contributes to Increased Virulence
Universally Sloppy Parameter Sensitivities in Systems Biology Models
Ancient Exaptation of a CORE-SINE Retroposon into a Highly Conserved Mammalian Neuronal Enhancer of the Proopiomelanocortin Gene

My Picks from ScienceDaily

Fossil Data Plugs Gaps In Current Knowledge, Study Shows:

Researchers have shown for the first time that fossils can be used as effectively as living species in understanding the complex branching in the evolutionary tree of life.

Cilia: Small Organelles, Big Decisions:

Johns Hopkins researchers say they have figured out how human and all animal cells tune in to a key signal, one that literally transmits the instructions that shape their final bodies. It turns out the cells assemble their own little radio antenna on their surfaces to help them relay the proper signal to the developmental proteins “listening” on the inside of the cell.

Avoiding Sweets May Spell A Longer Life, Study In Worms Suggests:

A new study in Cell Metabolism reveals that worms live to an older age when they are unable to process the simple sugar glucose. Glucose is a primary source of energy for the body and can be found in all major dietary carbohydrates as a component of starches and other forms of sugar, including sucrose (table sugar) and lactose.

My Picks from ScienceDaily

Engineers Study Brain Folding In Higher Mammals:

Engineers at Washington University in St. Louis are finding common ground between the shaping of the brain and the heart during embryonic development.

Fungus Genome Yielding Answers To Protect Grains, People And Animals:

Why a pathogen is a pathogen may be answered as scientists study the recently mapped genetic makeup of a fungus that spawns the worst cereal grains disease known and also can produce toxins potentially fatal to people and livestock.

Large-scale Head Lice Finding Kits Effective:

Working with parents and schools to provide a bug busting approach to head lice is helping to reduce infestation levels, tackle health inequalities and reduce healthcare costs, according to a review in the Journal of Clinical Nursing.

Hydrothermal Vents: Hot Spots Of Microbial Diversity:

Thousands of new kinds of marine microbes have been discovered at two deep-sea hydrothermal vents off the Oregon coast by scientists at the MBL (Marine Biological Laboratory) and University of Washington’s Joint Institute for the Study of Atmosphere and Ocean.

Census Of Protein Architectures Offers New View Of History Of Life:

The present can tell you a lot about the past, but you need to know where to look. A new study appearing this month in Genome Research reveals that protein architectures – the three-dimensional structures of specific regions within proteins – provide an extraordinary window on the history of life.

ClockQuotes

Nobody can be exactly like me. Sometimes even I have trouble doing it.
– Tallulah Bankhead

My Picks from ScienceDaily

Genes Determine Mate Choice, At Least For Fat Tailed Dwarf Lemurs:

How do we choose our mates? For quite some time now, scientists suspect that it is not for looks or fashion, neither for love or sympathy. It may be the genes that determine our preference for certain males or females. A new study provides support for this idea by looking at lemurs in Madagascar.

Beyond A ‘Speed Limit’ On Mutations, Species Risk Extinction:

Harvard University scientists have identified a virtual “speed limit” on the rate of molecular evolution in organisms, and the magic number appears to be 6 mutations per genome per generation — a level beyond which species run the strong risk of extinction as their genomes lose stability.

Genetic Differences In Clover Make One Type Toxic:

That clover necklace you make for your child could well be a ring of poison. That’s because some clovers have evolved genes that help the plant produce cyanide — to protect itself against little herbivores, such as snails, slugs and voles, that eat clover. Other clover plants that do not make cyanide are found in climates with colder temperatures. So, in picking your poison, er, clover, ecology and geography play important roles.

Spouses Often Mirror Each Other’s Health Habits:

If one spouse exercises, quits smoking, stops drinking alcohol, receives a flu shot, or undergoes a cholesterol screening, the other spouse is more likely to do the same, according to a new study in Health Services Research.

Galapagos Hawk’s Evolutionary History Illuminated:

Scientists at the University of Missouri-St. Louis used DNA sequences from feather lice to study how island populations of their host, the Galápagos Hawk might have colonized the Galápagos islands, home to the endangered and declining raptor.

Today’s Carnivals

I and the Bird #59 is up on Naturalist Notebook
Carnival of Space #23 is up on Advanced nanotechnology
Philosophia Naturalis #14 is up on Dynamics of Cats
The latest Change of Shift is up at Madness: tales of an emergency room nurse

Blogrolling for Today

All but one species


DNApes


Stephen Fry


Correlations


Sauropod Vertebra Picture of the Week


SWOP East Sex Workers Outreach Project

ClockQuotes

Time is a file that wears and makes no noise.
– English proverb

SBC-NC’08

2008NCSBClogo200.pngThere are already 80 registered participants for the Science Blogging Conference with almost four months still to go! Reserve a place for yourself by registering today!

New in Science Publishing, etc.

From Pierre, we hear about a new system for calculating individuals’ research impact – Publish Or Perish, based on Google Scholar.
Deepak, Pedro, Mark and Deepak again take a first look at Clinical Trials Hub and like what they see.
Jeff published a paper, but his Mom was more worried (in the comments) about the way he looks, with Congrats relegated to the afterthought.
SXSW Podcast on Open Knowledge vs. Controlled Knowledge has now been posted online. Worth a listen.
There is an article in Wired on science video sites, including JoVE, LabAction and SciVee and Attila provides deeper commentary.
Is “prokaryotic” an outdated term? Join the discussion (on this paper).
I love this quote: One Plos One Equals Three… in the sense that Open Access publishing is synergetically better.
Yes, I’ll be there.
A new Open Access physics journal.

Nerdy Licence Plates

Karl of Inoculated Mind blog just got a new set of plates for his truck and, of course, the plates read: INOCUL8.
Karl now wants to collect examples of nerdy, sciency licence plates and perhaps make a set on Flickr (similar to Carl Zimmer‘s Science Tatoo Gallery), so send him the picture of yours (of course you have one!) or your lab mates’ plates.
Some time ago, when I used to park at the Genetics/Entomology parking lot at NCSU, there were several regulars there with plates that read RNA, FRUITFLY, ILUVBUGS, PHEROMON, etc. I actually do not have a vanity plate, although the NC limit of 8 letters would accomodate COTURNIX.
Jonathan Eisen has a licence plate that says PLOS ORG. Now that is dedication to Open Access! Perhaps next time I need new plates I can get a PLOS one as well (his is California, mine would be North Carolina).
So, what do you have?