Monthly Archives: August 2008

My picks from ScienceDaily

Exploring The Function Of Sleep:

Is sleep essential? Ask that question to a sleep-deprived new parent or a student who has just pulled an “all-nighter,” and the answer will be a grouchy, “Of course!” But to a sleep scientist, the question of what constitutes sleep is so complex that scientists are still trying to define the essential function of something we do every night. A study published this week in PLoS Biology by Chiara Cirelli and Giulio Tononi addresses this pressing question.

‘Perfect Pitch’ In Humans Far More Prevalent Than Expected:

Researchers at the University of Rochester’s Eastman School of Music and Department of Brain and Cognitive Sciences have developed a unique test for perfect pitch, and have found surprising results.

Undergrads’ Amazon Trip Yields A Treasure Trove Of Diversity:

A group of Yale undergraduates have discovered dozens of potentially beneficial bioactive microorganisms within plants they collected in the Amazon rain forest, including several so genetically distinct that they may be the first members of new taxonomical genera.

Looking Beyond The Drug Receptor For Clues To Drug Effectiveness:

Antipsychotic drugs that are widely used to treat schizophrenia and other problems may not work as scientists have assumed, according to findings from Duke University Medical Center researchers that could lead to changes in how these drugs are developed and prescribed.

Consumers Can Predict Inflation As Well As Professional Economists:

When it comes to predicting the rate of inflation, professional economists might tell consumers, “Your guess is as good as mine.” Research by a Kansas State University professor shows that household surveys predict the inflation rate fairly accurately and as well as professional economists. The pros employ statistics like the unemployment rate, money supply growth and exchange rate changes. Consumers participating in surveys are more likely to think about how much they spent at the grocery store that week.

Is Extinction Or Diversity On The Rise? Study Of Islands Reveals Surprising Results:

It’s no secret that humans are having a huge impact on the life cycles of plants and animals. UC Santa Barbara’s Steven D. Gaines and fellow researcher Dov Sax decided to test that theory by studying the world’s far-flung islands.

How Does Bluetongue Virus Survive Through The Winter?:

Bluetongue virus – which infects livestock – reached Northern Europe for the first time. Some people thought that the outbreak would be limited to that particular year, as winter was expected to kill off the midges that host and spread the disease, bringing the threat of infection to an end. In actuality, the disease escalated in the following year, spreading to the UK. So, how did the virus survive the winter?

Fishing Technology Letting Turtles Off The Hook:

Alternative fishing technology has been shown to save turtles while not affecting fish catches, according to a report released by WWF and the Inter-American Tropical Tuna Commission (IATTC).

Men Defy Stereotypes In Defining Masculinity:

Contrary to stereotypes about sexual performance and masculinity, men interviewed in a large international study reported that being seen as honorable, self-reliant and respected was more important to their idea of masculinity than being seen as attractive, sexually active or successful with women.

Secret Of Newborn’s First Words Revealed:

A new study could explain why “daddy” and “mommy” are often a baby’s first words – the human brain may be hard-wired to recognize certain repetition patterns.

Why Do Eyelids Sag With Age? Mystery Is Solved:

Many theories have sought to explain what causes the baggy lower eyelids that come with aging, but UCLA researchers have now found that fat expansion in the eye socket is the primary culprit.

Java Gives Caffeine-naive A Boost, Too:

New research from the University of Alberta in Edmonton, Canada, shows that–for women–the caffeine advantage is indeed everything it’s cracked up to be. Females who don’t drink coffee can get just as much of a caffeine boost as those who sip it regularly, according to a study in the latest edition of Nutrition Research.

Trouble Quitting? New Smoking Study May Reveal Why:

A new study from researchers at the University of Pittsburgh and Carnegie Mellon University sheds light on why smokers’ intentions to quit “cold turkey” often fizzle out within days or even hours.

Blogrolling for Today

I was lost but now I live here

Academic Productivity

Victoria Stodden

Leftward Ho

Mind Surfing With Shecky


Neurotonics: a PT team blog

Rationale Thoughts

New and Exciting in PLoS ONE

Small Scattered Fragments Do Not a Dwarf Make: Biological and Archaeological Data Indicate that Prehistoric Inhabitants of Palau Were Normal Sized:

Current archaeological evidence from Palau in western Micronesia indicates that the archipelago was settled around 3000-3300 BP by normal sized populations; contrary to recent claims, they did not succumb to insular dwarfism. Previous and ongoing archaeological research of both human burial and occupation sites throughout the Palauan archipelago during the last 50 years has produced a robust data set to test hypotheses regarding initial colonization and subsequent adaptations over the past three millennia. Close examination of human burials at the early (ca. 3000 BP) and stratified site of Chelechol ra Orrak indicates that these were normal sized individuals. This is contrary to the recent claim of contemporaneous “small-bodied” individuals found at two cave sites by Berger et al. (2008). As we argue, their analyses are flawed on a number of different analytical levels. First, their sample size is too small and fragmentary to adequately address the variation inherent in modern humans within and outside of Palau. Second, the size and stature of all other prehistoric (both older and contemporaneous) skeletal assemblages found in Palau fall within the normal parameters of modern human variation in the region, indicating this was not a case of insular dwarfism or a separate migratory group. Third, measurements taken on several skeletal elements by Berger et al. may appear to be from smaller-bodied individuals, but the sizes of these people compares well with samples from Chelechol ra Orrak. Last, archaeological, linguistic, and historical evidence demonstrates a great deal of cultural continuity in Palau through time as expected if the same population was inhabiting the archipelago. Prehistoric Palauan populations were normal sized and exhibit traits that fall within the normal variation for Homo sapiens–they do not support the claims by Berger et al. (2008) that there were smaller-bodied populations living in Palau or that insular dwarfism took place such as may be the case for Homo floresiensis.

The Neural Correlates of Desire:

In an event-related fMRI study, we scanned eighteen normal human subjects while they viewed three categories of pictures (events, objects and persons) which they classified according to desirability (desirable, indifferent or undesirable). Each category produced activity in a distinct part of the visual brain, thus reflecting its functional specialization. We used conjunction analysis to learn whether there is a brain area which is always active when a desirable picture is viewed, regardless of the category to which it belongs. The conjunction analysis of the contrast desirable > undesirable revealed activity in the superior orbito-frontal cortex. This activity bore a positive linear relationship to the declared level of desirability. The conjunction analysis of desirable > indifferent revealed activity in the mid-cingulate cortex and in the anterior cingulate cortex. In the former, activity was greater for desirable and undesirable stimuli than for stimuli classed as indifferent. Other conjunction analyses produced no significant effects. These results show that categorizing any stimulus according to its desirability activates three different brain areas: the superior orbito-frontal, the mid-cingulate, and the anterior cingulate cortices.

Climate Warming, Marine Protected Areas and the Ocean-Scale Integrity of Coral Reef Ecosystems:

Coral reefs have emerged as one of the ecosystems most vulnerable to climate variation and change. While the contribution of a warming climate to the loss of live coral cover has been well documented across large spatial and temporal scales, the associated effects on fish have not. Here, we respond to recent and repeated calls to assess the importance of local management in conserving coral reefs in the context of global climate change. Such information is important, as coral reef fish assemblages are the most species dense vertebrate communities on earth, contributing critical ecosystem functions and providing crucial ecosystem services to human societies in tropical countries. Our assessment of the impacts of the 1998 mass bleaching event on coral cover, reef structural complexity, and reef associated fishes spans 7 countries, 66 sites and 26 degrees of latitude in the Indian Ocean. Using Bayesian meta-analysis we show that changes in the size structure, diversity and trophic composition of the reef fish community have followed coral declines. Although the ocean scale integrity of these coral reef ecosystems has been lost, it is positive to see the effects are spatially variable at multiple scales, with impacts and vulnerability affected by geography but not management regime. Existing no-take marine protected areas still support high biomass of fish, however they had no positive affect on the ecosystem response to large-scale disturbance. This suggests a need for future conservation and management efforts to identify and protect regional refugia, which should be integrated into existing management frameworks and combined with policies to improve system-wide resilience to climate variation and change.

Bi-Directional Sexual Dimorphisms of the Song Control Nucleus HVC in a Songbird with Unison Song:

Sexually dimorphic anatomy of brain areas is thought to be causally linked to sex differences in behaviour and cognitive functions. The sex with the regional size advantage (male or female) differs between brain areas and species. Among adult songbirds, males have larger brain areas such as the HVC (proper name) and RA (robust nucleus of the arcopallium) that control the production of learned songs. Forest weavers (Ploceus bicolor) mated pairs sing a unison duet in which male and female mates learn to produce identical songs. We show with histological techniques that the volume and neuron numbers of HVC and RA were ≥1.5 times larger in males than in females despite their identical songs. In contrast, using in-situ hybridizations, females have much higher (30-70%) expression levels of mRNA of a number of synapse-related proteins in HVC and/or RA than their male counterparts. Male-typical and female-typical sexual differentiation appears to act on different aspects of the phenotypes within the same brain areas, leading females and males to produce the same behaviour using different cellular mechanisms.

Evaluation of Two Methods to Estimate and Monitor Bird Populations:

Effective management depends upon accurately estimating trends in abundance of bird populations over time, and in some cases estimating abundance. Two population estimation methods, double observer (DO) and double sampling (DS), have been advocated for avian population studies and the relative merits and short-comings of these methods remain an area of debate. We used simulations to evaluate the performances of these two population estimation methods under a range of realistic scenarios. For three hypothetical populations with different levels of clustering, we generated DO and DS population size estimates for a range of detection probabilities and survey proportions. Population estimates for both methods were centered on the true population size for all levels of population clustering and survey proportions when detection probabilities were greater than 20%. The DO method underestimated the population at detection probabilities less than 30% whereas the DS method remained essentially unbiased. The coverage probability of 95% confidence intervals for population estimates was slightly less than the nominal level for the DS method but was substantially below the nominal level for the DO method at high detection probabilities. Differences in observer detection probabilities did not affect the accuracy and precision of population estimates of the DO method. Population estimates for the DS method remained unbiased as the proportion of units intensively surveyed changed, but the variance of the estimates decreased with increasing proportion intensively surveyed. The DO and DS methods can be applied in many different settings and our evaluations provide important information on the performance of these two methods that can assist researchers in selecting the method most appropriate for their particular needs.

Random Drift versus Selection in Academic Vocabulary: An Evolutionary Analysis of Published Keywords:

The evolution of vocabulary in academic publishing is characterized via keyword frequencies recorded in the ISI Web of Science citations database. In four distinct case-studies, evolutionary analysis of keyword frequency change through time is compared to a model of random copying used as the null hypothesis, such that selection may be identified against it. The case studies from the physical sciences indicate greater selection in keyword choice than in the social sciences. Similar evolutionary analyses can be applied to a wide range of phenomena; wherever the popularity of multiple items through time has been recorded, as with web searches, or sales of popular music and books, for example.

Unusual Repertoire of Vocalizations in the BTBR T+tf/J Mouse Model of Autism:

BTBR T+ tf/J (BTBR) is an inbred mouse strain that displays social abnormalities and repetitive behaviors analogous to the first and third diagnostic symptoms of autism. Here we investigate ultrasonic vocalizations in BTBR, to address the second diagnostic symptom of autism, communication deficits. As compared to the commonly used C57BL/6J (B6) strain, BTBR pups called more loudly and more frequently when separated from their mothers and siblings. Detailed analysis of ten categories of calls revealed an unusual pattern in BTBR as compared to B6. BTBR emitted high levels of harmonics, two-syllable, and composite calls, but minimal numbers of chevron-shaped syllables, upward, downward, and short calls. Because body weights were higher in BTBR than B6 pups, one possible explanation was that larger thoracic size was responsible for the louder calls and different distribution of syllable categories. To test this possibility, we recorded separation calls from FVB/NJ, a strain with body weights similar to BTBR, and 129X1/SvJ, a strain with body weights similar to B6. BTBR remained the outlier on number of calls, displaying low numbers of complex, upward, chevron, short, and frequency steps calls, along with high harmonics and composites. Further, developmental milestones and growth rates were accelerated in BTBR, indicating an unusual neurodevelopmental trajectory. Overall, our findings demonstrate strain-specific patterns of ultrasonic calls that may represent different lexicons, or innate variations in complex vocal repertoires, in genetically distinct strains of mice. Particularly intriguing is the unusual pattern of vocalizations and the more frequent, loud harmonics evident in the BTBR mouse model of autism that may resemble the atypical vocalizations seen in some autistic infants.

Genetic Architecture of Hybrid Male Sterility in Drosophila: Analysis of Intraspecies Variation for Interspecies Isolation:

The genetic basis of postzygotic isolation is a central puzzle in evolutionary biology. Evolutionary forces causing hybrid sterility or inviability act on the responsible genes while they still are polymorphic, thus we have to study these traits as they arise, before isolation is complete. Isofemale strains of D. mojavensis vary significantly in their production of sterile F1 sons when females are crossed to D. arizonae males. We took advantage of the intraspecific polymorphism, in a novel design, to perform quantitative trait locus (QTL) mapping analyses directly on F1 hybrid male sterility itself. We found that the genetic architecture of the polymorphism for hybrid male sterility (HMS) in the F1 is complex, involving multiple QTL, epistasis, and cytoplasmic effects. The role of extensive intraspecific polymorphism, multiple QTL, and epistatic interactions in HMS in this young species pair shows that HMS is arising as a complex trait in this system. Directional selection alone would be unlikely to maintain polymorphism at multiple loci, thus we hypothesize that directional selection is unlikely to be the only evolutionary force influencing postzygotic isolation.

Gender Differences in the Risk of HIV Infection among Persons Reporting Abstinence, Monogamy, and Multiple Sexual Partners in Northern Tanzania:

Monogamy, together with abstinence, partner reduction, and condom use, is widely advocated as a key behavioral strategy to prevent HIV infection in sub-Saharan Africa. We examined the association between the number of sexual partners and the risk of HIV seropositivity among men and women presenting for HIV voluntary counseling and testing (VCT) in northern Tanzania. Clients presenting for HIV VCT at a community-based AIDS service organization in Moshi, Tanzania were surveyed between November 2003 and December 2007. Data on sociodemographic characteristics, reasons for testing, sexual behaviors, and symptoms were collected. Men and women were categorized by number of lifetime sexual partners, and rates of seropositivity were reported by category. Factors associated with HIV seropositivity among monogamous males and females were identified by a multivariate logistic regression model. Of 6,549 clients, 3,607 (55%) were female, and the median age was 30 years (IQR 24-40). 939 (25%) females and 293 (10%) males (p<0.0001) were HIV seropositive. Among 1,244 (34%) monogamous females and 423 (14%) monogamous males, the risk of HIV infection was 19% and 4%, respectively (p<0.0001). The risk increased monotonically with additional partners up to 45% (p<0.001) and 15% (p<0.001) for women and men, respectively with 5 or more partners. In multivariate analysis, HIV seropositivity among monogamous women was most strongly associated with age (p<0.0001), lower education (p<0.004), and reporting a partner with other partners (p = 0.015). Only age was a significant risk factor for monogamous men (p = 0.0004). Among women presenting for VCT, the number of partners is strongly associated with rates of seropositivity; however, even women reporting lifetime monogamy have a high risk for HIV infection. Partner reduction should be coupled with efforts to place tools in the hands of sexually active women to reduce their risk of contracting HIV.

Today’s carnivals

Grand Rounds, Volume 4, #49 are up on Rural Doctoring
Carnival of the Green #142 is up on Life Goggles
The 139th Carnival of Homeschooling is up on Life Nurturing Education

Victoria Stodden: Open Source Science-Open Research License

From SciFoo 08:

Victoria Stodden discusses her efforts to create a new license for scientific research which covers both publication and data. She discusses the motivations behind the new license and the issues brought up by releasing scientific research and data under and open source license.
Copyright 2008 O’Reilly News. All Rights Reserved. Filmed at Scifoo 2008 at the Googleplex in Mountain View, CA by Tim O’Brien.

How do you know in advance what you will discover so you can say so in your grant proposal?

Jean-Claude Bradley reviews Happy Accidents: Serendipity in Modern Medical Breakthroughs by Morton A. Meyers. Morton says:

An applicant for a research grant is expected to have a clearly defined program for a period of three to five years. Implicit is the assumption that nothing unforeseen will be discovered during that time and, even if something were, it would not cause distraction from the approved line of research. Yet the reality is that many medical discoveries were made by researchers working on the basis of a fallacious hypothesis that led them down an unexpected fortuitous path.

Jean-Claude adds:

We can share our failed experiments. We can share our research plans. We can discuss science freely admitting what we don’t know. We can record our talks at closed meetings and make them public. We can initiate and participate in serious scientific conversations going on in the blogosphere without worrying about everyone’s title and rank.
Basically, we can collaborate in ways that are most conducive to serendipitous discoveries. The free social software, databases and other infrastructure now available make this information exchange easier than ever.

Court win for Fair Use

Judge Rules That Content Owners Must Consider Fair Use Before Sending Takedowns:

A judge’s ruling today is a major victory for free speech and fair use on the Internet, and will help protect everyone who creates content for the Web. In Lenz v. Universal (aka the “dancing baby” case), Judge Jeremy Fogel held that content owners must consider fair use before sending takedown notices under the Digital Millennium Copyright Act (“DMCA”).

Some interesting data about Impact Factors

For those of you interested in the science publishing business, there is an interesting paper out about Impact Factors, where they do the math to try to explain why the IFs are apparentluy always rising from year to year, and to figure out the differences between disciplines. They remain agnostic pretty much about the whole hot controversy about the validity of IF, but their data explain some facts about IF that can be added, IMHO, into the growing lists of reasons why IF should be abandoned:
Althouse, B.M., West, J.D., Bergstrom, C.T., Bergstrom, T. (in press). Differences in impact factor across fields and over time. Journal of the American Society for Information Science and Technology DOI: 10.1002/asi.20936

The bibliometric measure impact factor is a leading indicator of journal influence, and impact factors are routinely used in making decisions ranging from selecting journal subscriptions to allocating research funding to deciding tenure cases. Yet journal impact factors have increased gradually over time, and moreover impact factors vary widely across academic disciplines. Here we quantify inflation over time and differences across fields in impact factor scores and determine the sources of these differences. We find that the average number of citations in reference lists has increased gradually, and this is the predominant factor responsible for the inflation of impact factor scores over time. Field-specific variation in the fraction of citations to literature indexed by Thomson Scientific’s Journal Citation Reports is the single greatest contributor to differences among the impact factors of journals in different fields. The growth rate of the scientific literature as a whole, and cross-field differences in net size and growth rate of individual fields, have had very little influence on impact factor inflation or on cross-field differences in impact factor.

Christina looks at their math and summarizes the paper as well:

Impact factors of journals are a perennial discussion topic – used by libraries (with other measures) for collection development and by researchers to decide where to publish. They’re also mis-used, abused, and misunderstood. But this article isn’t about all that. This article looks at whether the impact factors are going up, what aspect of the impact factor provides the greatest contribution or explains the increase, and if the increase is different in different disciplinary categories?

My picks from ScienceDaily

Cells In Eye Could Help Control Sleep:

A set of nerve cells in the eye control our levels of sleepiness according to the brightness of our surroundings, Oxford University researchers have discovered. The cells directly regulate the activity of sleep centres in the brain, providing a new target for the development of drugs to control sleep and alertness.

New Evidence Debunks ‘Stupid’ Neanderthal Myth:

Research by UK and American scientists has struck another blow to the theory that Neanderthals (Homo neanderthalensis) became extinct because they were less intelligent than our ancestors (Homo sapiens). The research team has shown that early stone tool technologies developed by our species, Homo sapiens, were no more efficient than those used by Neanderthals.

Monkeys Enjoy Giving To Others, Study Finds:

Researchers at the Yerkes National Primate Research Center, Emory University, have shown capuchin monkeys, just like humans, find giving to be a satisfying experience. This finding comes on the coattails of a recent imaging study in humans that documented activity in reward centers of the brain after humans gave to charity.

Polar Bears Found Swimming Miles From Alaskan Coast:

An aerial survey by government scientists in Alaska’s Chukchi Sea has recently found at least nine polar bears swimming in open water – with one at least 60 miles from shore – raising concern among wildlife experts about their survival.

Even Seaweeds Get Sunburned:

It is red, it burns and itches: a sunburn on our skin. However, too much sun is not only bad for humans. Many plants react sensitively to an increased dose of ultraviolet radiation, too. Yet they are dependent on sunlight. With the help of pigments absorbing solar energy and light, plants produce their vitally important building blocks by means of photosynthesis.


Children begin by loving their parents; after a time they judge them; rarely, if ever, do they forgive them.
– Oscar Wilde

Obligatory Readings of the Day: Science Outreach and Online Behavior

Science promotion is not science outreach, damn it!:

We’ve all encountered this: the science communication department at a large university is usually devoted to marketing the research of that particular university. The so-called “outreach” products of such departments – the public talks, articles, and events for school groups – are all forced to suit this purpose. Mediocre research is described in glowing terms as “world-class” or “ground-breaking”. Poor communicators are put forward again and again so that they can be seen as a leader in their field.
This is promotion, not outreach. Describing this as educating about science is like saying that a car commercial is designed to teach viewers about engine design.

Interview with Eva Amsen:

There are different kinds of science outreach: One type of outreach is aimed at elementary and high school students to get them interested in a career in science. Another type is aimed at people who don’t work in science and never will work in science but who are curious about the world and like hearing about science. That is my favourite kind of outreach, because to a certain extent everybody *is* interested in science. People will say that they don’t like science, but what they don’t like is the memory of sitting in a science classroom in high school. Once you point out that there is science involved in many of he things they read about in the news every day – alternative fuels, stem cell therapy, forensics – it suddenly becomes interesting and you have an eager audience wanting to learn more about DNA fingerprinting or energy conversion.

You go to war with the data you have:

My interest in these experiments has less to do with questions of political polarization and more to do with interest in international news. Are internet readers more inclined to look for information about other countries, since they’ve got such a wealth of information at their fingertips? Or are they more inclined towards information on their home countries, since they can easily choose to avoid international news. Extrapolating from Pew’s data suggests that wired readers might consult more sources and perhaps consume a more diverse diet; Farrell’s research points to a strong homophily effect, which suggests the possibility of geographic cocooning.
Guess I’ll need to design my own experiments using whatever data I can as a proxy to indirectly answer the question… and hope other researchers find other data and other methods to challenge my assumptions.

New and Exciting in PLoS Biology and PLoS Medicine

Monday night – time to check out the new articles in PLoS Biology and PLoS Medicine:
Is Sleep Essential?:

Everybody knows that sleep is important, yet the function of sleep seems like the mythological phoenix: “Che vi sia ciascun lo dice, dove sia nessun lo sa” (“that there is one they all say, where it may be no one knows,” Wolfgang Amadeus Mozart and Lorenzo da Ponte [1790], Così fan tutte). But what if the search for an essential function of sleep is misguided? What if sleep is not required but rather a kind of extreme indolence that animals indulge in when they have no more pressing needs, such as eating or reproducing? In many circumstances sleeping may be a less dangerous choice than roaming around, wasting energy and exposing oneself to predators. Also, if sleep is just one out of a repertoire of available behaviors that is useful without being essential, it is easier to explain why sleep duration varies so much across species [1-4]. This “null hypothesis” [5-7] would explain why nobody has yet identified a core function of sleep. But how strong is the evidence supporting it? And are there counterexamples?

SciCurious reviews this article as well.
Whisker-Mediated Texture Discrimination:

Our sense of touch provides information about nearby objects that can affect us in an immediate way. Texture, a central component of touch, is sensed quickly, even before an object is explored to measure its size, shape, or identity. To learn how contact with a surface produces a sensation of texture, many laboratories have examined the whisker system of rodents. Touch sensed through the whiskers in rodents works differently than touch sensed through the fingertips in primates. Touch receptors in the fingertips are distributed in a continuous sheet; this spatial distribution of inputs gives important signals about texture [1]. In contrast, rodents use a set of roughly 30 whiskers on each side of the snout, palpating surfaces through a 5-15 Hz forward-backward motion known as “whisking.” When a whisker’s tip or shaft makes contact with a texture, its movement changes; whisker motion signals report to the brain what the whiskers have contacted.

Where Does Bluetongue Virus Sleep in the Winter?:

Bluetongue virus (BTV) is spread by the bites of Culicoides midges (Figure 1), and can infect ruminant livestock such as cattle, sheep, and goats, wild ruminants such as deer, and camelids. Some infected animals develop the disease known as bluetongue, with clinical signs ranging from apathy and weight loss to swollen heads, tender feet and death (Figure 2). Historically a tropical and subtropical disease, bluetongue has become a regular visitor to southern Europe in the last decade [1,2]. Although growth in the global trade in livestock may have increased the frequency with which exotic viruses are introduced into Europe, the increasing tendency of those introduced strains to persist and spread is probably best explained by changes to the European climate [3], and several direct and indirect links between climate and BTV transmission have been identified [2]. BTV reached northern Europe for the first time in 2006, and affected around 2,000 holdings before reports ceased in early January 2007. The outbreak then re-emerged months later [4] and spread to a further 45,000 holdings by the end of the year, making it the most economically damaging outbreak of bluetongue ever seen [2,5].

SAW: Breaking Down Barriers between Art and Science:

The path to specialization of knowledge starts early. By the time children leave primary school, they have already been taught to view subjects like biology, art, and social studies as unrelated disciplines rather than as interlocking pieces that together lay the foundation for a deeper understanding of the world. The divisions between science, the arts, and the humanities are reinforced in high school, where each subject is taught by a different instructor under pressure to “teach to the test,” a practice that further isolates subjects, stifles inquisitiveness, and quells creativity. By the time we become specialists as adults, our ability to recognize connections between disciplines tends to diminish even further–often at a price. If during this process, we lose the ability to communicate with other groups of specialists (for example, chemists, physicists, and mathematical modelers) or with those who have not had any formal science education beyond high school (which would include many taxpayers, politicians, and policy makers), if we become unresponsive to the needs of society, then our value to society becomes compromised. And the question arises: how do we break down these barriers or prevent them from becoming established in the first place, without compromising the standards of the different disciplines?

Effect of the California Tobacco Control Program on Personal Health Care Expenditures:

Large state tobacco control programs have been shown to reduce smoking and would be expected to affect health care costs. We investigate the effect of California’s large-scale tobacco control program on aggregate personal health care expenditures in the state. Cointegrating regressions were used to predict (1) the difference in per capita cigarette consumption between California and 38 control states as a function of the difference in cumulative expenditures of the California and control state tobacco control programs, and (2) the relationship between the difference in cigarette consumption and the difference in per capita personal health expenditures between the control states and California between 1980 and 2004. Between 1989 (when it started) and 2004, the California program was associated with $86 billion (2004 US dollars) (95% confidence interval [CI] $28 billion to $151 billion) lower health care expenditures than would have been expected without the program. This reduction grew over time, reaching 7.3% (95% CI 2.7%-12.1%) of total health care expenditures in 2004. A strong tobacco control program is not only associated with reduced smoking, but also with reductions in health care expenditures.

Assassin Bugs and Bats

New and Exciting in PLoS ONE

There are 12 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. Here are my own picks for the week – you go and look for your own favourites:
Individual Differences in the Amount and Timing of Salivary Melatonin Secretion:

The aim of this study was to examine individual differences in a large sample of complete melatonin profiles not suppressed by light and search for possible associations between the amount and timing of melatonin secretion and a multitude of lifestyle variables. The melatonin profiles were derived from saliva samples collected every 30 minutes in dim light from 85 healthy women and 85 healthy men aged 18-45 years. There was a large individual variability in the amount of melatonin secreted with peak values ranging from 2 to 84 pg/ml. The onset of melatonin secretion ranged from 18:13 to 00:26 hours. The use of hormonal birth control, reduced levels of employment, a smaller number of days on a fixed sleep schedule, increased day length and lower weight were associated with an increased amplitude of melatonin secretion. The use of hormonal birth control, contact lenses, a younger age, and lower ratings of mania and paranoia were associated with a longer duration of melatonin secretion. An earlier occurrence of the onset of melatonin secretion was associated with an earlier wake time, more morningness and the absence of a bed partner. Lifestyle and behavioral variables were only able to explain about 15% of the individual variability in the amount of melatonin secretion, which is likely because of a substantial genetic influence on the levels of melatonin secretion.

Predominant Role of Host Genetics in Controlling the Composition of Gut Microbiota:

The human gastrointestinal tract is inhabited by a very diverse symbiotic microbiota, the composition of which depends on host genetics and the environment. Several studies suggested that the host genetics may influence the composition of gut microbiota but no genes involved in host control were proposed. We investigated the effects of the wild type and mutated alleles of the gene, which encodes the protein called pyrin, one of the regulators of innate immunity, on the composition of gut commensal bacteria. Mutations in MEFV lead to the autoinflammatory disorder, familial Mediterranean fever (FMF, MIM249100), which is characterized by recurrent self-resolving attacks of fever and polyserositis, with no clinical signs of disease in remission. A total of 19 FMF patients and eight healthy individuals were genotyped for mutations in the MEFV gene and gut bacterial diversity was assessed by sequencing 16S rRNA gene libraries and FISH analysis. These analyses demonstrated significant changes in bacterial community structure in FMF characterized by depletion of total numbers of bacteria, loss of diversity, and major shifts in bacterial populations within the Bacteroidetes, Firmicutes and Proteobacteria phyla in attack. In remission with no clinical signs of disease, bacterial diversity values were comparable with control but still, the bacterial composition was substantially deviant from the norm. Discriminant function analyses of gut bacterial diversity revealed highly specific, well-separated and distinct grouping, which depended on the allele carrier status of the host. This is the first report that clearly establishes the link between the host genotype and the corresponding shifts in the gut microbiota (the latter confirmed by two independent techniques). It suggests that the host genetics is a key factor in host-microbe interaction determining a specific profile of commensal microbiota in the human gut.

My picks from ScienceDaily

How ‘Secondary’ Sex Characters Can Drive The Origin Of Species:

The ostentatious, sometimes bizarre qualities that improve a creature’s chances of finding a mate may also drive the reproductive separation of populations and the evolution of new species, say two Indiana University Bloomington biologists.

Elephant Legs Are Much Bendier Than Shakespeare Thought:

Throughout history, elephants have been thought of as ‘different’. Shakespeare, and even Aristotle, described them as walking on inflexible column-like legs. And this myth persists even today. Which made John Hutchinson from The Royal Veterinary College, London, want to find out more about elephants and the way they move. Are they really that different from other, more fleet-footed species? Are their legs as rigid and ‘columnar’ as people had thought?

Life Isn’t 2-D, So Why Should Our Encyclopedias Be?:

Biologists and biochemists are now able to access 3D images of biomacromolecules underlying biological functions and disease. Rather than relying on text to provide the understanding of biomacromolecule structures, a collaborative website called Proteopedia now provides a new resource by linking written information and three-dimensional structural information.

Why Wind Turbines Can Mean Death For Bats:

Power-generating wind turbines have long been recognized as a potentially life-threatening hazard for birds. But at most wind facilities, bats actually die in much greater numbers. Now, researchers reporting in Current Biology, a Cell Press journal, on August 26th think they know why.

Animals Adapt Their Vocal Signals To Social Situations:

A special August issue of the Journal of Comparative Psychology, published by the American Psychological Association, presents a host of studies that investigate the way that animals adapt their calls, chirps, barks and whistles to their social situation.

To those who do not like the democratization of knowledge

[Comic strip taken from Unshelved]
The anti-technology curmudgeons are back. Not just worrying about technology in classrooms (for which Dave has a great response), but culture in general.
Nice to see a couple of good responses to the doom-and-gloom crowd.
First we: DIGITAL_NATIVES by Jonathan Imme:

There used to be a time when we would be called ‘nerds’ or ‘techies’. Strange people with a near-obsessive compulsion to embrace new technology, and who’d rather communicate with their friends online than offline. People for whom the Internet itself was the ultimate source of information for solving any kind of problem whatsoever.
However, society is now slowly coming to terms with the fact that a whole generation is growing up that has only ever known the ‘digital age’, and has therefore entirely accepted the digital way of doing things. We call ourselves the Digital Native generation.
Then again, we Digital Natives are not only characterized by our self-sufficient attitude to new technologies. We also have a different concept of the culture of information, communication and entertainment. We listen to music and watch films online. The fact that we also use file-swapping sites comes from the simple fact that we’re not about to pay for content on principle – no matter how exciting it may be.
Looking to the long-term, and in the light of our contemporary grasp of copyright law and our extensive recommendation and exchange activities among our friends, industry moguls would be better off sending us not to prison but to the business development units of the entertainment companies.

Then, in WIRED (also in print, I hear): The Critics Need a Reboot. The Internet Hasn’t Led Us Into a New Dark Age by David Wolman:

When in doubt, blame the latest technology. Socrates thought the advent of writing would wreak havoc on the powers of the mind. Christian theologians denounced the printing press as the work of the devil. The invention of the telephone was supposed to make letter-writing extinct, and the arrival of the train — and later the car and plane — was going to be the death of community.
Now comes a technological bogeyman for the 21st century, this one responsible for a supposed sharp uptick in American shallowness and credulity: the Internet and its digital spawn.
Or consider the Public Library of Science: By breaking the publishing industry’s choke hold on the circulation of scientific information, this powerful online resource arms scientists and the masses alike with the same data, accelerating new discoveries and breakthroughs. Not exactly the kind of effect one would expect from a technology that’s threatening to turn us into philistines.

Why teaching evolution is dangerous

It is so nice teaching biology to adults when there are no (obvious) Creationists in the classroom. It does not always happen that way – I have had a couple of cases in the past – but this time it was really nice as I could freely cover all topics deeply within an evolutionary framework (not always seen in my public notes, though, as I try to gauge the class first and then decide how overtly to talk ebout everything in evolutionary terms). It is always a conundrum. If there is a potential resentment of my lectures, I have to thread carefully. I have to remember that I am not trying to turn them into biologists, but that I am trying to make them think for themselves and to understand evolution even if they do not want to ‘believe’ it for religious reasons. Thus, I first teach about cell, heredity and development, which gives them (and me) tools for coverage of evolution. Then I explain evolution using insects as an example before ending with a “humans, of course” as well. Then I cover Origin of Life, evolution of diversity and current diversity. But I do not leave evolution behind when I move on to ecology, behavior and physiology either. More easily this time, but sometimes a little more ‘sneakily’ if I know I have Creationists in class.
So, I know exactly how difficult it is to teach even younger students – they are more likely to act rebelliously (adults will go along in order to get the grade and move on) and they are still more under the influence of parents and do not have enough world experiences. I admire high school teachers who teach Biology in areas of the country in which Creationism is rampant and most of the kids are likely to be a priori biased against it.
A week after the nice column by Olivia Judson about the necessity of teaching evolution in school, NYTimes once again visits this question, with a very nice article about Mr.Campbell, a biology teacher in Florida, one of the people who was involved in the latest science curriculum battles in that state this year.
Like a game of whack-a-mole, Creationist get defeated in court in one state, just to resurface in another state and start the process all over again. As they keep losing in courts, they are forced to dilute their message, and adopt the language that may, on the surface, seem OK, unless you know exactly what THEY mean by that language and how that language is supposed to be a wedge that lets religious instruction into public school science classes.
The NYTimes article was brought to my attention by Jonathan Eisen, Tom Levenson, Kent and Mike Dunford and then I saw that many other bloggers have picked up on it since.
Ed Darrell points out the competitive advantage this gives the rest of the world and how local the problem of Creationism is.
David Rea sees that the NCSE responses to Well’s “Ten questions to ask your biology teacher about evolution” (also accessible at the NYT site next to the article) are far too nuanced and likely to go over the heads of most Americans, and suggests to use them to teach the meaning of words, and the meaning of evolutionary concepts – they cannot stand for themselves but can be useful as a starting point for a classroom discussion.
Peter Dawson Buckland responds to one of the frequent misrepresentations of evolution that shows up in the article (voiced by a Creationist teacher in the same school as Campbell) and gives a vote to pragmatism over philosophical accuracy. PZ Myers disagrees and insists on absolute accuracy. John Hawks points out that the Mickey Mouse is not an example of evolution – with which I agree: like Pokemon (and perhaps Spore), it is an example of gradual metamorphosis, in this case exacerbated by the fact that change is not induced by the natural environment but by human marketers.
As of this writing, the article has 342 comments on the NYTimes site, mainly by people who liked it and who – some clumsily, others with more expertise – try to explain the difference between scientific and colloquial usages of “theory” and other answers to those age-old questions that Creationists have been asking for a century or more already (and bored everyone to death, including myself, as the answers are readily available online, in books, etc.).
One comment that I particularly liked was this one:

I second comment #3. Bless Mr. Campbell. He was my high school biology teacher, and this article only begins to illustrate all the ways in which he is an amazing teacher. He constantly challenges his students to think for themselves, to analyze, and to test hypotheses rather than simply accept things at face value. He was the first teacher who ever taught me how, not what, to think, and Mr. Campbell is the reason I am now a biologist, studying evolutionary biology. Thank you, Mr. Campbell, and all biology teachers like you, who, in teaching evolution well, nurture the natural curiosity in young minds.
— Natalie Wright, Gainesville, FL

But some of the best commentary is right there in the article – words of Campbell himself. See this:

“If I do this wrong,” Mr. Campbell remembers thinking on that humid spring morning, “I’ll lose him.”

Mr. Campbell knows how tricky this process is. You cannot bludgeon kids with truth (or insult their religion, i.e., their parents and friends) and hope they will smile and believe you. Yes, NOMA is wrong, but is a good first tool for gaining trust. You have to bring them over to your side, gain their trust, and then hold their hands and help them step by step. And on that slow journey, which will be painful for many of them, it is OK to use some inaccuracies temporarily if they help you reach the students. If a student, like Natalie Wright who I quoted above, goes on to study biology, then he or she will unlearn the inaccuracies in time. If most of the students do not, but those cutesy examples help them accept evolution, then it is OK if they keep some of those little inaccuracies for the rest of their lives. It is perfectly fine if they keep thinking that Mickey Mouse evolved as long as they think evolution is fine and dandy overall. Without Mickey, they may have become Creationist activists instead. Without belief in NOMA they would have never accepted anything, and well, so be it. Better NOMA-believers than Creationists, don’t you think?
But for me, the key quote of the article is this one:

“If you see something you don’t understand, you have to ask ‘why?’ or ‘how?’ ” Mr. Campbell often admonished his students at Ridgeview High School.

Education is a subversive activity that is implicitly in place in order to counter the prevailing culture. And the prevailing culture in the case of Campbell’s school, and many other schools in the country, is a deeply conservative religious culture.
There are many ideals or “values” that conservatives and liberals share. Freedom, strength, honesty, generosity, courage, responsibility, etc. are equally valued by people of all ideologies. The conservatives and liberals may define or understand them a little differently, they may order them differently according to importance, and they may deduce some very different policy proposals out of them, but in general they all agree that these are good human values.
But there is one human trait where the two ideologies differ. That is Obedience. For conservatives, this is a positive human trait. For liberals, it is viewed quite negatively. Why?
Because the two ideologies view time and history differently.
Conservatives see history as a story of decline from some mythical Golden Age which, depends who you ask, may be the Garden of Eden, or middle ages when Church and State were one and the same, or late 19th century USA with robber barons in charge, or 1930s Italy and Germany when Business and State were one and the same (and kept all the “Others” down), or 1950s when women were sent to the kitchen. They feel like the future is bleak and that their duty is to slow down and stop the decline, or reverse it if they can.
Their belief that world is dangerous is a part of this mindset – they always think that the world is more to be feared now than it was in the mystical past. Corporate media help them in this – switch off the TV and tell me: how many violent crimes, tragic accidents, horrific natural disasters, and war terrors, have you personally witnessed today in real life? Yesterday, the day before, throughout your life? How come you are still alive? Oh, but the media wants to deliver you to the advertising so you will buy whatever will alleviate your fears today and make life worth living yet another day.
For us (liberals), the history is seen as an arrow of progress: every generation has a better life than the previous one, every generation puts some work and effort, and if needed fight, to make the world a better place for the next generation. We want to foster and continue this trend. For this to happen, each generation needs to break with the parents’ worldview to some extent. What is considered “normal” part of life for one’s elders, may not be so for the youngsters who take a serious look at it. Most importantly, each generation brings in another level of equality, bringing up a group that was institutionally pushed down during history, be it women, gays, blacks, etc.
Now, the word “equality” is understood differently by the two ideologies. It does not mean handicapping everyone to have the same no matter what their talents and hard work should earn them. It does not mean preventing people from attaining success. It means allowing people to go to the top regardless of who their parents were. If you made it, your kids should not get a leg-up because of that – they need to start from zero and try to make it as well. Or fail. But more importantly, it does not matter if your parents are rich or poor, white or black, US-born or foreign-born, religious or not, if you are male or female, straight or gay – you should have the exact same social and instititutional support in your strivings toward success.
Also, the measure of success in dollars is a pretty conservative notion – you can be dirt-poor yet be successful, consider yourself successful and be regarded by others as successful along other criteria, e.g., generosity, skill, talent. And the accidents of your birth should not be a factor.
In a worldview which sees everything as a zero-sum game, equality is anathema. If one goes up, this means someone else is going down. If women are gaining, this means men are losing. If Blacks are gaining equality, this means Whites are losing. If you see the world as hierarchical this is the inevitable outcome of your worldview.
Thus, the most essential thing that conservatives want to conserve is the social organization, including all of its power relationships, with the white, American, Christian, (officially) straight, rich, adult, male humans on top of everyone else. If that is your worldview, of course what normal people consider progress will look like doom to you. After all, we measure progress by how big strides we have made in eliminating the old power structures that used to subdue groups of people under others.
Another way to call this is authoritarianism, in which one group asserts authority over others and does whatever it takes to keep it that way.
An important aspect of the conservative hierarchy is the authority of old over the young. The stereotype of an Old Wise Man Who Remembers The Golden Age of Yore. He who can bring that Golden Age back. The top of the hierarchy. Thus, obedience to His authority is essential for preservation of the hierarchical power structure. Thus, conservatives do not like education, they prefer “training”. They start early by training little kids, by methods bordering on abuse, to unquestioningly obey their elders.
The school should be a place to instill obedience (measure of success in rolling back progress) as well as to train for jobs that bring in the money (monetary measure of success). Thus, conservatives tend to fight against the liberal academia and hate to be told that Reality has a Liberal Bias. And most importantly, they fight against science education as it directly undermines the obedience.
See what Mr.Campbell is doing? Kids who were taught obedience know they are supposed to unquestioningly obey their elders, which includes their parents, priests and teachers. But Campbell puts them in a mental bind – they want to obey him but he is telling them things opposite from what their parents and priests are saying. Who to listen to? As a result of this exercise, they unlearn obedience. A red-flag danger for the conservatives. Their kids have been corrupted – they were, gasp, taught to think for themselves. And we all know what independent thinking brings about – progress! We can’t have that, can we?!
This is why Creationism is such an important plank in the conservative political strategy – it undermines the teaching of independent thinking. The asking of How and Why questions. All the stuff that each generation needs in order to analyze and reject their parent’s generation’s regressive worldview. Doom!

My picks from ScienceDaily

Tiny Cellular Antennae Trigger Neural Stem Cells:

Yale University scientists today reported evidence suggesting that the tiny cilia found on brain cells of mammals, thought to be vestiges of a primeval past, actually play a critical role in relaying molecular signals that spur creation of neurons in an area of the brain involved in mood, learning and memory.

Picking Out Specific Sounds In A Complex Scene: Researchers Study ‘Cocktail Party Effect’, Measure Auditory Dynamics Of Selective Attention:

Call it the cocktail party effect: how an individual can participate in a one-on-one conversation within a cluster of people, switch to another, pick up important comments while tuning out others, change topics and return to the first conversation.

Starting Kindergarten Later Gives Students Only A Fleeting Edge, Study Finds:

New research challenges a growing trend toward holding kids out of kindergarten until they’re older, arguing that academic advantages are short-lived and come at the expense of delaying entry into the workforce and other costs.

Part Of The In-group? A Surprising New Strategy Helps Reduce Unhealthy Behaviors:

Public health campaigns intended to reduce unhealthy behaviors like binge drinking and eating junk food often focus on the risks of those behaviors. But a new study in the Journal of Consumer Research suggests a relatively simple but surprisingly effective strategy to improve consumer health.

79 Million US Adults Have Medical Bill Problems Or Are Paying Off Medical Debt:

The proportion of working-age Americans who have medical bill problems or who are paying off medical debt climbed from 34 percent to 41 percent between 2005 and 2007, bringing the total to 72 million, according to recent survey findings from The Commonwealth Fund. In addition, 7 million adults age 65 and over also had problems paying medical bills, for a total of 79 million adults with medical bill problems or medical debt.


The way you explore complex ecosystems is you try lots of things and you hope that everybody who fails, fails informatively.
– Clay Shirky

Carrboro Creative Coworking – the pricing list released

You know I am excited about Carrboro Creative Coworking. Looking at the pricing list which was released today, I think there will be a place for me there I can afford….

Multiple dimensions!

Totally awesome: Dimensions:

Nine chapters, two hours of maths, that take you gradually up to the fourth dimension. Mathematical vertigo guaranteed!

Hat-tip: quixote

My picks from ScienceDaily

Foul Owls Use Feces To Show They Are In Fine Feather:

Some years ago, within the Department of Conservation Biology of the Estación Biológica de Doñana (EBD-Consejo Superior de Investigaciones Científicas; Seville, Spain), a recently established group (colloquially named the Night Ecology Group) started to explore the possibility of visual communication in crepuscular and nocturnal birds.

Exploding Chromosomes Fuel Research About Evolution Of Genetic Storage:

Human cells somehow squeeze two meters of double-stranded DNA into the space of a typical chromosome, a package 10,000 times smaller than the volume of genetic material it contains.

Fish Cancer Gene Linked To Pigment Pattern That Attracts Mates:

Though skin cancer is deadly to male fish, it also has one perk: The black melanoma splotches arise from attractive natural markings that lure female mates. A new study published in the Proceedings of the National Academy of Sciences this week shows that the melanoma gene can be conserved in swordtail fish because of its beneficial role in sexual selection.

Addiction Treatment Proves Successful In Animal Weight Loss Study:

Vigabatrin, a medication proposed as a potential treatment for drug addiction by scientists at the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory, also leads to rapid weight loss and reduced food intake according to a new animal study from the same research group.

Insomnia: Changing Your Bedtime Habits Could Help:

Many people sleep better when they are on holiday and wish that they could sleep as well all the time. But according to the German Institute for Quality and Efficiency in Health Care (IQWiG), it is not only being free of daily worries that can make a difference to sleep. Good bedtime habits can help people to sleep well all year round. Medication provides short-term relief at best.

Snacks In Small Packages May Lead To Overeating:

Tempting treats are being offered in small package sizes these days, presumably to help consumers reduce portion sizes. Yet new research found that people actually consume more high-calorie snacks when they are in small packages than large ones. And smaller packages make people more likely to give in to temptation in the first place.

There is no need for a ‘Creepy Treehouse’ in using the Web in the classroom

I love the way Web works! So, I was on FriendFeed earlier today and I saw through this link there that Paul Jones posted a note on Pownce (on which I am registered but never check) about this article in Raleigh N&O:
An iPod Touch for each student?

A Chapel Hill middle school could become the first in the country to give an iPod to every teacher and student, an experiment that would challenge teachers and administrators to ensure the hand-held devices are used as learning tools, not toys.
It’s still not clear how the iPod Touches would be used at Culbreth Middle School. And school officials know that students may use the iPod Touches more to download the new Jonas Brothers single than to tap the riches of human knowledge. But Principal Susan Wells says that to dismiss the technology as a distraction or a gimmick ignores today’s tech-driven world.
“It’s a world we better figure out, because we can’t ask our students to come into a classroom, put those things aside and sit in a row and think we’re interesting,” she said.
“We’re just not that interesting.”
Mountain View High School in Meridian, Idaho, banned the use of all iPods last year when they suspected students were using them to cheat. Principal Aaron Maybon said some students would record audio of them saying answers to test questions. Then they’d wear a baggy sweater with the iPod concealed underneath and run the ear buds through the sleeve to their wrist. When they needed an answer, they would rest their head on their hand.
“We did have to take a hard-line approach to that,” Maybon said. “You can restrict all kinds of stuff and you can drive yourself nuts trying to police all of it. They [Culbreth] are probably kind of opening themselves up to something.”
Wells said Culbreth teachers are eager to start using iPods in class.
“These teachers say this pilot signals their commitment to our students to meet them where they are, as opposed to where the teachers are comfortable,” Wells said.
“They state their commitment to teach 21st-century skills, because technology is the future for students and teachers.”

Yup, this year, when both of my kids are out of Culbreth school!
A couple of days before, John Dupuis posted (check a long comment thread on FriendFeed) a link to When Professors Create Social Networks for Classes, Some Students See a ‘Creepy Treehouse’

A growing number of professors are experimenting with Facebook, Twitter, and other social-networking tools for their courses, but some students greet an invitation to join professors’ personal networks with horror, seeing faculty members as intruders in their private online spaces. Recognizing that, some professors have coined the term “creepy treehouse” to describe technological innovations by faculty members that make students’ skin crawl.

The ‘Creepy Treehouse’ is defined as, among else:

n. A situation in which an authority figure or an institutional power forces those below him/her into social or quasi-social situations.
With respect to education, Utah Valley University student Tyrel Kelsey describes, “creepy treehouse is what a professor can create by requiring his students to interact with him on a medium other than the class room tools. [E.g.] requiring students to follow him/her on peer networking sites such as Twitter or Facebook.”

So, which is it? Good or bad? I think a lot of people (including many teachers and administrators) are not familiar with the Web sufficiently enough to see it is more than one fuzzy big Scary Place. Thus they get confused when they hear Good News and Bad News one after another – which is it? If you think that Web is a single thing, you will not understand the distinctions between different parts of it and different ways of using it. Thus, either you dedicate yourself to learn more about it, or you pick one side (Good or Bad) and stick to it.
There is a difference between using online techologies in teaching and teachers inviting students to friend them on Facebook. The former is acknowledgment that kids today have a very different worldview and behavior and we need to learn it and use it for education. The latter is personal intrusiveness.
Not using the Web in teaching these days is a criminal act of mis-education. It is preparing the 21st century kids for a 19th century world. FAIL.
Or, as David Warlick says:

I’m pretty sure that it was Alan Kay who said that, “Technology is anything that was invented after you were born.” Does it have to stay that way? At what point does it stop being the technology and become the medium — and become transparent?
This is a barrier for us, this sense that we’re striving to modernize classrooms by using more technology. I still do not think that the kids do this. When they go out and buy the latest game system, they are not buying the latest technology. They’re buying better games. They are buying better experiences.
Folks out there who are making valuable and sustainable uses of technology, do you still think of it as integrating technology? If not, when did that stop? When did it become sustainable?
I guess for me, it happened when I started thinking about my job as entirely about inventing and communicating, rather than helping people integrate technology.

Pet food with a high Impact Factor

Nature%20pet%20food.jpgBut, how many fonts are out there anyway?
Or perhaps Nature is secretly diversifying its operations ;-)
But what would be the formula for calculating Impact Factor of pet food?
d = maximal distance of projectile vomiting
t = time between the onset of feeding and onset of projectile vomiting
m = total mass of vomited material as percent of ingested food
k = coefficient that normalizes the pet size to 15kg regardless of the actual size of the animal.
So, how does one plug these values in?

Blogospheric responses to the Biden pick

A wide range of opinions:
Melissa McEwan: Biden and Shocker: Women Less Enthusiastic Than Men About Biden
Melissa McEwan: Obama’s small change
Jesse Taylor: Obama/Biden
Ezra Klein: Winning the argument
Joe Trippi: Stay Loose Joe, Stay Loose
See the comment thread on the Intersection: Obama Picks Joe Biden and also It’s 3AM And Joe Biden’s Giving Foriegn Policy Advice To Barack Obama
John Lynch: Obama, Biden & the Progressive Future
Ed Brayton: Thoughts on Biden as VP
Greg Laden: Obama will Pick Biden as VP on Saturday. and Obama Picks VP Running Mate
Josh Rosenau: Bidenmania
Pam Spaulding: And Obama’s running mate is…Joe Biden, Republicans hail Biden selection, The debut of the Obama/Biden ticket and Quote of the day – John McCain’s seven kitchen tables.

10 Alternative Ways To Follow Democratic Convention News

Links by Myrna the Minx, something for you to bookmark and use. I’ll probably use FriendFeed and visit some of my favourite blogs (including Pam and the Blenders who will be there – see the NYTimes article about the bloggers at the Convention).


It’s not that I’m afraid to die, I just don’t want to be there when it happens.
– Woody Allen


I have no competing interests, nobody is paying me to say nice things, but I have helped set up a CollectiveX group site and it was easy and I like its functionality a lot:

BlogTogether 2008 Backyard Barbecue

Update: Register, login and edit the wiki if you intend to show up tonight.
Anton just sent a message to the Triangle blogging community:

The annual BlogTogether Backyard Barbecue is this Saturday, August 23 from 5pm on, at my home in Durham. I’ll provide a cold keg of Carolina Brewery suds, a hot grill and tasty pulled pork barbecue, and a deck perfect for conversing into the night. More details at

In NC next weekend? Join us!

My picks from ScienceDaily

With Skate Eyes, Scientists Peer Into Human Disease:

Paradoxically, the photoreceptor cells in our retinas release more of their neurotransmitter, glutamate, in the dark, when there is nothing to see, than they do in the light. This is doubly surprising since although glutamate is a major signaling molecule in the retina and throughout the central nervous system, it is also a potent cytotoxin that, in large doses, can kill nearby cells.

New Algorithm Significantly Boosts Routing Efficiency Of Networks:

A time-and-money-saving question shared by commuters in their cars and networks sharing ever-changing Internet resources is: “What’s the best way to get from here to there?”

New And Improved Test For West Nile Virus In Horses:

A new test for West Nile virus in horses that could be modified for use on humans and wildlife may help track the spread of the disease, according to an article in the September issue of the Journal of Medical Microbiology.

Insomnia: Changing Your Bedtime Habits Could Help:

Many people sleep better when they are on holiday and wish that they could sleep as well all the time. But according to the German Institute for Quality and Efficiency in Health Care (IQWiG), it is not only being free of daily worries that can make a difference to sleep. Good bedtime habits can help people to sleep well all year round. Medication provides short-term relief at best.

Hormone Replacement Therapy Improves Sleep, Sexuality And Joint Pain In Older Women:

One of the world’s longest and largest trials of hormone replacement therapy (HRT) has found that post-menopausal women on HRT gain significant improvements in quality of life.

Is It Possible To Teach Experience? European Researchers Say Yes:

Business veterans claim you cannot teach ‘experience’, but European researchers say you can. The team developed software that helps players acquire real-life skills and realistic experiences through game playing. But this game is no executive toy.

Genome Of Simplest Animal Reveals Ancient Lineage, Confounding Array Of Complex Capabilities:

As Aesop said, appearances are deceiving–even in life’s tiniest critters. From first detection in the 1880s, clinging to the sides of an aquarium, to its recent characterization by the U.S. Department of Energy Joint Genome Institute (DOE JGI), a simple and primitive animal, Trichoplax adhaerens, appears to harbor a far more complex suite of capabilities than meets the eye.

Genes And Nutrition Influence Caste In Unusual Species Of Harvester Ant:

Researchers trying to determine whether nature or nurture determines an ant’s status in the colony have found a surprising answer. Both.


Egotism, n. Doing the New York Times crossword puzzle with a pen.
– Ambrose Bierce

Veep? WTF?!

They (meaning: CNN) say it’s Biden. Yuck! The old-school hawk whose only ‘supposed strength’ is foreign policy which he proceeded to show he is ignorant of every night on TV during the 1990s spouting nonsense about the Balkans.

New and Exciting in PLoS ONE

There are 7 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. Here are my own picks for the week – you go and look for your own favourites:

Continue reading

Looking for the mouse…

Watch what Clay Shirky said at Web 2.0 Expo SF 2008 (transcript here):

The quote that everyone likes, for a good reason, is the following:

I was having dinner with a group of friends about a month ago, and one of them was talking about sitting with his four-year-old daughter watching a DVD. And in the middle of the movie, apropos nothing, she jumps up off the couch and runs around behind the screen. That seems like a cute moment. Maybe she’s going back there to see if Dora is really back there or whatever. But that wasn’t what she was doing. She started rooting around in the cables. And her dad said, “What you doing?” And she stuck her head out from behind the screen and said, “Looking for the mouse.”
Here’s something four-year-olds know: A screen that ships without a mouse ships broken. Here’s something four-year-olds know: Media that’s targeted at you but doesn’t include you may not be worth sitting still for.
It’s also become my motto, when people ask me what we’re doing– from now on, that’s what I’m going to tell them: We’re looking for the mouse.

Kevin Kelly likes it. Bjoern Brembs says:

Most scientists have not made the transition of this four-year-old, yet.

The thing is….it’s not just screens. I keep looking for the mouse and the “post comment” button whenever I read a book!

Aggregator of RSS feeds about Gynecology

Vedran keeps cranking these at an incredible rate (the first numbers indicate these aggregators are quite comprehensive and the feedback is that they are useful) – here is the latest one: Aggregator of RSS feeds about Gynecology

Open Source Science – Science and Sharing

Michael Nielsen’s talk at SciFoo’08:


This blog is slowly approaching a nice round number – 10,000 comments. I know this is not Pharyngula where this would take an hour or two to fill, but still, we can get the remaining 200+ comments in over the next few days, can’t we?
The person who posts the 10,000th non-spam comment will get a prize – something (your choice exactly what) from the A Blog Around The Clock store.

My picks from ScienceDaily

Face Recognition: Nurture Not Nature:

Researchers have discovered that our society can influence the way we recognise other people’s faces. Because face recognition is effortlessly achieved by people from all different cultures it was considered to be a basic mechanism universal among humans. However, by using analyses inspired by novel brain imaging technology, researchers at the University of Glasgow have discovered that cultural differences cause us to look at faces differently.

Manes, Trains And Antlers Explained: How Showy Male Traits Evolved:

For Charles Darwin, the problem of the peacock’s tail, in light of his theory of natural selection, was vexing in the extreme. Indeed, in 1860, writing to Asa Gray, his most ardent American champion, Darwin confessed: “The sight of a feather in a peacock’s tail, whenever I gaze at it, makes me sick!” In his struggle to explain why such extravagant and seemingly burdensome features existed, the great English naturalist struck upon the idea of sexual selection — that showy traits such as the Peacock’s ornamentation were an advantage in the mating game that outweighed other disadvantages.

Shipwrecks On Coral Reefs Harbor Unwanted Species:

Shipwrecks on coral reefs may increase invasion of unwanted species, according to a recent U.S. Geological Survey study. These unwanted species can completely overtake the reef and eliminate all the native coral, dramatically decreasing the diversity of marine organisms on the reef. This study documents for the first time that a rapid change in the dominant biota on a coral reef is unambiguously associated with man-made structures.

Genetics Reveals Big Fish That Almost Got Away:

Researchers from the University of Hawaii, the Wildlife Conservation Society, Smithsonian Tropical Research Institute, National Marine Fisheries Service and Projecto Meros do Brazil discovered a new species of fish–a grouper that reaches more than six feet in length and can weigh nearly 1,000 pounds. This newly discovered species can be found roaming the tropical reefs of the Eastern Pacific Ocean.

Kids With Pets Grow Up To Be Snorers:

A predisposition to adult snoring can be established very early in life. New research describes possible childhood risk factors, including exposure to animals, early respiratory or ear infections and growing up in a large family.

Research Shows Pollsters How The Undecided Will Vote:

As the American Presidential election approaches, pollsters are scrambling to predict who will win. A study by a team of researchers at The University of Western Ontario, Canada, and the University of Padova, Italy, may give pollsters a new way to determine how the undecided will vote, even before the voters know themselves.

Trees Kill Odors And Other Emissions From Poultry Farms:

Planting just three rows of trees around poultry farms can cut nuisance emissions of dust, ammonia, and odors from poultry houses and aid in reducing neighbor complaints, according to scientists from the University of Delaware.

Dietary Supplements For Horses, Dogs And Cats Need Better Regulation, New Report Says:

The growing use of animal dietary supplements has raised several concerns, including the safety of specific supplements and the approaches taken to determine their safeness.

The 21st Century Workplace is wherever you and your laptop happen to be

12 New Rules of Working You Should Embrace Today. As you know, point #4 is one of my pet peeves:

4. People don’t have to be in an office. This is the one I wish most businesses would get, right now, right away. It’s so obvious once you get away from the traditional mindset. Traditionally, people worked in offices (and of course most still do). They go into the office, do their work, go to meeting, process paperwork, chat around the watercooler, clock out and go home.
These days, more and more, that’s not necessary. With mobile computing, the cloud, online apps and collaborative processes, work can be done from anywhere, and often is. More people are telecommuting. More people are working as freelancers or consultants. More businesses are allowing people to work from anywhere — not just telecommuting from home, but literally anywhere in the world. People are forming small businesses who have never met, who live on different continents. People have meetings through Skype or Basecamp group chat. They collaborate through wikis and Google apps.
If you are stuck in the traditional mindset, think hard about what things really need to be done in an office. Sometimes there are legitimate reasons for working in an office, but often those barriers have other solutions you just haven’t explored yet.
The advantages of a decentralized workplace are many. Workers who have more freedom are happier, and often more passionate about their work. They enjoy collaborating with others who are smart and talented, and work is no longer drudgery. Flexible schedules work well for many people’s lifestyles. Mobile computing is actually good for many types of businesses where people need to be on the go. And what really matters isn’t that the worker is present, but that the work is being done.

Today’s carnivals

Edition #82 of I and the Bird is up on Sycamore Canyon
Friday Ark #205 is up on Modulator

Science Olympics!

My favourite discipline is citation gymnastics! What is yours? Can you invent a new sport?

Blogrolling for Today

The Edger

Pondering blather


Scientist Carrie

Effortless Incitement

Boston Globe on Open Science

Boston Globe has an interesting article about Open Science, citing the routine list of worries that usually get associated with this idea, e.g., :

But in the world of science – where promotions, tenure, and fortune rest on publishing papers in prestigious journals, securing competitive grants, and patenting discoveries – it’s a brazen, potentially self-destructive move. To many scientists, leaving unfinished work and ideas in the open seems as reckless as leaving your debit card and password at a busy ATM machine.

But, as John Hawks says:

I think that’s a pretty simplistic rendering of how scientific credit is assigned. It ignores all the factors that depend not on your results but on networking. Who you know may be vastly more important than what you do.
I think that if more researchers were independent (not tied to someone else’s lab) and if they spent less time grant-writing, we’d see more open collaborations. Right now the biggest barrier to openness is centralization.

Light-Responsive genes in rice

Friendly blogger Pamela Roland, the author of Tomorrow’s Table: Organic Farming, Genetics, and the Future of Food which I am reading right now (and which was recently reviewed in PLoS Biology), has just had a paper published in PLoS Genetics:
Identification and Functional Analysis of Light-Responsive Unique Genes and Gene Family Members in Rice

Rice, a model monocot, is the first crop plant to have its entire genome sequenced. Although genome-wide transcriptome analysis tools and genome-wide, gene-indexed mutant collections have been generated for rice, the functions of only a handful of rice genes have been revealed thus far. Functional genomics approaches to studying crop plants like rice are much more labor-intensive and difficult in terms of maintaining the plants than when studying Arabidopsis, a model dicot. Here, we describe an efficient method for dissecting gene function in rice and other crop plants. We identified light response-related phenotypes for ten genes, the functions for which were previously unknown in rice. We also carried out co-expression analysis of 72 genes involved in specific biochemical pathways connected in lines carrying mutations in these ten genes. This analysis led to the identification of a novel set of genes likely involved in these pathways. The rapid progress of functional genomics in crops will significantly contribute to overcoming a food crisis in the near future.


I was born not knowing and have only had a little time to change that here and there.
– Richard Feynman

Tribute to Marbles and OJ

by Coturnietta…

Another Kevin’s photo-essay from China

Kevin has just posted another photo-rich report from his herpetology survey in China. Lots of pictures of Chinese landscape, Chinese people, Chinese food, and yes – cool Chinese animals.

New and Exciting in PLoS ONE

There are 10 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. Here are my own picks for the week – you go and look for your own favourites:
A Dominant X-Linked QTL Regulating Pubertal Timing in Mice Found by Whole Genome Scanning and Modified Interval-Specific Congenic Strain Analysis:

Pubertal timing in mammals is triggered by reactivation of the hypothalamic-pituitary-gonadal (HPG) axis and modulated by both genetic and environmental factors. Strain-dependent differences in vaginal opening among inbred mouse strains suggest that genetic background contribute significantly to the puberty timing, although the exact mechanism remains unknown. We performed a genome-wide scanning for linkage in reciprocal crosses between two strains, C3H/HeJ (C3H) and C57BL6/J (B6), which differed significantly in the pubertal timing. Vaginal opening (VO) was used to characterize pubertal timing in female mice, and the age at VO of all female mice (two parental strains, F1 and F2 progeny) was recorded. A genome-wide search was performed in 260 phenotypically extreme F2 mice out of 464 female progeny of the F1 intercrosses to identify quantitative trait loci (QTLs) controlling this trait. A QTL significantly associated was mapped to the DXMit166 marker (15.5 cM, LOD = 3.86, p<0.01) in the reciprocal cross population (C3HB6F2). This QTL contributed 2.1 days to the timing of VO, which accounted for 32.31% of the difference between the original strains. Further study showed that the QTL was B6-dominant and explained 10.5% of variation to this trait with a power of 99.4% at an alpha level of 0.05.The location of the significant ChrX QTL found by genome scanning was then fine-mapped to a region of ~2.5 cM between marker DXMit68 and rs29053133 by generating and phenotyping a panel of 10 modified interval-specific congenic strains (mISCSs). Such findings in our study lay a foundation for positional cloning of genes regulating the timing of puberty, and also reveal the fact that chromosome X (the sex chromosome) does carry gene(s) which take part in the regulative pathway of the pubertal timing in mice.

Elusive Origins of the Extra Genes in Aspergillus oryzae:

The genome sequence of Aspergillus oryzae revealed unexpectedly that this species has approximately 20% more genes than its congeneric species A. nidulans and A. fumigatus. Where did these extra genes come from? Here, we evaluate several possible causes of the elevated gene number. Many gene families are expanded in A. oryzae relative to A. nidulans and A. fumigatus, but we find no evidence of ancient whole-genome duplication or other segmental duplications, either in A. oryzae or in the common ancestor of the genus Aspergillus. We show that the presence of divergent pairs of paralogs is a feature peculiar to A. oryzae and is not shared with A. nidulans or A. fumigatus. In phylogenetic trees that include paralog pairs from A. oryzae, we frequently find that one of the genes in a pair from A. oryzae has the expected orthologous relationship with A. nidulans, A. fumigatus and other species in the subphylum Eurotiomycetes, whereas the other A. oryzae gene falls outside this clade but still within the Ascomycota. We identified 456 such gene pairs in A. oryzae. Further phylogenetic analysis did not however indicate a single consistent evolutionary origin for the divergent members of these pairs. Approximately one-third of them showed phylogenies that are suggestive of horizontal gene transfer (HGT) from Sordariomycete species, and these genes are closer together in the A. oryzae genome than expected by chance, but no unique Sordariomycete donor species was identifiable. The postulated HGTs from Sordariomycetes still leave the majority of extra A. oryzae genes unaccounted for. One possible explanation for our observations is that A. oryzae might have been the recipient of many separate HGT events from diverse donors.

Progesterone from the Cumulus Cells Is the Sperm Chemoattractant Secreted by the Rabbit Oocyte Cumulus Complex:

Sperm chemotaxis in mammals have been identified towards several female sources as follicular fluid (FF), oviduct fluid, and conditioned medium from the cumulus oophorus (CU) and the oocyte (O). Though several substances were confirmed as sperm chemoattractant, Progesterone (P) seems to be the best chemoattractant candidate, because: 1) spermatozoa express a cell surface P receptor, 2) capacitated spermatozoa are chemotactically attracted in vitro by gradients of low quantities of P; 3) the CU cells produce and secrete P after ovulation; 4) a gradient of P may be kept stable along the CU; and 5) the most probable site for sperm chemotaxis in vivo could be near and/or inside the CU. The aim of this study was to verify whether P is the sperm chemoattractant secreted by the rabbit oocyte-cumulus complex (OCC) in the rabbit, as a mammalian animal model. By means of videomicroscopy and computer image analysis we observed that only the CU are a stable source of sperm attractants. The CU produce and secrete P since the hormone was localized inside these cells by immunocytochemistry and in the conditioned medium by enzyme immunoassay. In addition, rabbit spermatozoa express a cell surface P receptor detected by western blot and localized over the acrosomal region by immunocytochemistry. To confirm that P is the sperm chemoattractant secreted by the CU, the sperm chemotactic response towards the OCC conditioned medium was inhibited by three different approaches: P from the OCC conditioned medium was removed with an anti-P antibody, the attractant gradient of the OCC conditioned medium was disrupted by a P counter gradient, and the sperm P receptor was blocked with a specific antibody. We concluded that only the CU but not the oocyte secretes P, and the latter chemoattract spermatozoa by means of a cell surface receptor. Our findings may be of interest in assisted reproduction procedures in humans, animals of economic importance and endangered species.

Reverse and Conventional Chemical Ecology Approaches for the Development of Oviposition Attractants for Culex Mosquitoes:

Synthetic mosquito oviposition attractants are sorely needed for surveillance and control programs for Culex species, which are major vectors of pathogens causing various human diseases, including filariasis, encephalitis, and West Nile encephalomyelitis. We employed novel and conventional chemical ecology approaches to identify potential attractants, which were demonstrated in field tests to be effective for monitoring populations of Cx. p. quinquefasciatus in human dwellings. Immunohistochemistry studies showed that an odorant-binding protein from this species, CquiOBP1, is expressed in trichoid sensilla on the antennae, including short, sharp-tipped trichoid sensilla type, which house an olfactory receptor neuron sensitive to a previously identified mosquito oviposition pheromone (MOP), 6-acetoxy-5-hexadecanolide. CquiOBP1 exists in monomeric and dimeric forms. Monomeric CquiOBP1 bound MOP in a pH-dependent manner, with a change in secondary structure apparently related to the loss of binding at low pH. The pheromone antipode showed higher affinity than the natural stereoisomer. By using both CquiOBP1 as a molecular target in binding assays and gas chromatography-electroantennographic detection (GC-EAD), we identified nonanal, trimethylamine (TMA), and skatole as test compounds. Extensive field evaluations in Recife, Brazil, a region with high populations of Cx. p. quinquefasciatus, showed that a combination of TMA (0.9 µg/l) and nonanal (0.15 ng/µl) is equivalent in attraction to the currently used infusion-based lure, and superior in that the offensive smell of infusions was eliminated in the newly developed synthetic mixture.

Prefrontal Norepinephrine Determines Attribution of “High” Motivational Salience:

Intense motivational salience attribution is considered to have a major role in the development of different psychopathologies. Numerous brain areas are involved in “normal” motivational salience attribution processes; however, it is not clear whether common or different neural mechanisms also underlie intense motivational salience attribution. To elucidate this a brain area and a neural system had to be envisaged that were involved only in motivational salience attribution to highly salient stimuli. Using intracerebral microdialysis, we found that natural stimuli induced an increase in norepinephrine release in the medial prefrontal cortex of mice proportional to their salience, and that selective prefrontal norepinephrine depletion abolished the increase of norepinephrine release in the medial prefrontal cortex induced by exposure to appetitive (palatable food) or aversive (light) stimuli independently of salience. However, selective norepinephrine depletion in the medial prefrontal cortex impaired the place conditioning induced exclusively by highly salient stimuli, thus indicating that prefrontal noradrenergic transmission determines approach or avoidance responses to both reward- and aversion-related natural stimuli only when the salience of the unconditioned natural stimulus is high enough to induce sustained norepinephrine outflow. This affirms that prefrontal noradrenergic transmission determines motivational salience attribution selectively when intense motivational salience is processed, as in conditions that characterize psychopathological outcomes.

Young Scientist Challenge finalists announced

Working to empower students nationwide to experiment with science and technology, Discovery Education and 3M are hosting the 10th annual Young Scientist Challenge (YSC). Moving closer to recognizing “America’s Top Young Scientist of the Year” and “America’s Top Science Teacher of the Year,” Discovery Education and 3M announce this year’s finalists.

See them here.

Science Idol Cartoon Contest Winner

The Union of Concerned Scientists (UCS) announced the winner of its 2008 “Science Idol: Scientific Integrity Editorial Cartoon Contest,” which draws attention to the growing problem of political interference in federal government science.
Justin Bilicki, of Brooklyn, New York has earned the title of America’s “Science Idol” with his winning cartoon. It depicts a scientist presenting his research findings that conclude: “We are destroying the Earth.” Two government officials look on. The official holding a briefcase with money spilling out of it, says, “Could you kindly rephrase that in equivocal, inaccurate, vague, self-serving, and roundabout terms that we can all understand?”
See the winning cartoon at The original watercolor print has been put up for auction by the artist on the contest Web page, with all proceeds going to UCS.