My scientific specialty is chronobiology (circadian rhythms and photoperiodism), with additional interests in comparative physiology, animal behavior and evolution. I am not an MD so I cannot diagnose and treat your sleep problems. As well as writing this blog, I am also the Online Discussion Expert for PLoS. This is a personal blog and opinions within it in no way reflect the policies of PLoS. You can contact me at: Coturnix@gmail.com
The nicest post about ScienceOnline2010 to date was penned yesterday by Arikia Millikan, the former Overlord of Seed Scienceblogs.com (the image above is by her as well).
At the conference, Arikia will co-moderate the session on Web Science and I already introduced her here.
For those on the forefront of the development of the Web, the World Wide Web conference was an event that educated, inspired and forged partnerships by connecting people whose paths would otherwise never cross.
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The described enthusiasm and fervor of WWW conference attendees parallels the enthusiasm I observed of ScienceOnline participants.
And so I hereby dub the ScienceOnline conference, the Bonnaroo of the Blogosphere. I'm 23 and never attended Woodstock, but I think that as meaningful as it was to Sir Berners-Lee's generation, Bonnaroo probably is to mine. As important as it was to have a meeting in the late '90s to discuss and define the Web when it was in its infancy, it is as important to do so for the blogosphere today.
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Attending the ScienceOnline conference last year was an incredible experience that further solidified my decision to pursue my interest in the Web. It's a place where, if you're into science and you're into the Web, and these are the things that get you really excited academically, professionally and/or socially, you can learn what the game-changers in the field are up to and talking about, and talk about it with them, maybe become a game-changer yourself.
Buying books would be a good thing if one could also buy the time to read them in: but as a rule the purchase of books is mistaken for the appropriation of their contents.
So, hurry up. Write (or choose an existing) post in the area of evolutionary biology and send it in. Two lucky winners will get travel grants to ScienceOnline2010. Yes, we are full, and there are 101 people on the waiting list. But the two NESCent winners have their spots saved just for them!
My friend (I was the Best Man at his wedding, back in the 80s) is in Equatorial Guinea and the other day he took this dramatic photograph of a lightning:
Reminder: Deadline is December 1st at midnight EST!
Here are the submissions for OpenLab 2009 to date (under the fold). You can buy the 2006, 2007 and 2008 editions at Lulu.com. Please use the submission form to add more of your and other people's posts (remember that we are looking for original poems, art, cartoons and comics, as well as essays):
Make sure that the submitted posts are possible (and relatively easy) to convert into print. Posts that rely too much on video, audio, color photographs, copyrighted images, or multitudes of links just won't do.
Description: Students are a great resource for projects that require large numbers of volunteers. We will discuss examples of projects that combine student learning with authentic research and the power of blogs to connect students with projects. Discuss here.
B.Medicine 2.0 and Science 2.0--where do they intersect? - Walter Jessen
Description: Medicine 2.0 applications, services and tools are defined as Web-based services for healthcare consumers/patients, health professionals and biomedical researchers that use Web 2.0 technologies and/or semantic web and virtual reality approaches to enable and facilitate (1) social networking; (2) participation; (3) apomediation (guidance generated and available from peripheral mediators); (4) openness; and (5) collaboration within and between these user groups for the purposes of maintaining and/or restoring human health. How are these themes being applied in scientific research? What are the reasons some themes are better applied than others? How are researchers integrating Science 2.0 tools into their workflows? Do they offer an immediate benefit? Where could there be improvement? What are the social and cultural obstacles to widespread adoption of Medicine 2.0 and Science 2.0? Discuss here.
Description: Find free, scholarly, science stuff on the Internet, via your public or state library, or on the "free Web." Learn tips & tricks for getting full-text science research at all levels, through resources like DOAJ and NC Live (for those with a North Carolina library card; other states often offer free resources to library card holders). Find out about some options for storing science material at your academic institution's Institutional Repository. We will also talk about the broader access to material stored in institutional repositories and elsewhere on the Web. Discuss here.
Description: Over the past several years, the Internet has tangibly changed the way that movies and TV shows are produced and marketed. Blogs will call out ridiculous scientific errors found in stories and the critique can go viral very quickly; therefore, science advising is on the rise in an attempt to add some semblance of plausibility to your favorite flicks. As tools on the web continue to evolve, filmmakers and television creators are finding new ways to connect with and market to their viewers. For some shows, this has meant tapping into the science featured in their content, ranging from an exploration of the roots of the science that has been fictionalized to the expansion of a scientific topic explored in a documentary. In this session, we'll look at how online video and social networking tools are playing a part in connecting science, Hollywood and its fans. Discuss here.
Description: Introducing Deutsches Museum and Lampenfieber kids' science magazine.
- Science Media Centre and Sciblogs, New Zealand - Fabiana Kubke
Description: As part of the strategy to engage New Zealanders with science and technology the Ministry of Research, Science & Technology (MoRST) announced a three-year pilot Science & Technology Media Centre for New Zealand. The Science Media Centre, conceptualised on the success of the SMC's in the UK and Australia, serves as an independent source of expert comment and information for journalists covering science and technology. Its aim is to promote accurate, bias-free reporting on science and technology by helping the media work more closely with the scientific community. On September 30, 2009, SMC launched a major new science communication effort with Sciblogs, a network of science blogs covering everything from clinical health to climate change with 26 bloggers, including scientists from universities, Crown Research Institutes and private research organisations along the length of the country. It is the largest online hub for science-related content relevant to New Zealand. The Sciblogs platform is the first major implementation of the opensource Wordpress MU (multiple user) blogging system in New Zealand. Duscuss here.
- Social Networking and performance evaluation in scientific centers - John Hogenesch
Description: Analysis of collaboration between scientists. Discuss here.
Description: "Open Dinosaur Project":http://opendino.wordpress.com/ (ODP) was created to involve scientists and the public alike in developing a comprehensive database of dinosaur limb bone measurements, in order to investigate questions of dinosaur function and evolution. An untapped wealth of measurements is contained within the scientific literature, but a massive research team is needed to digitize these data into a usable form. With the rise of digital journals (many of which are open access) and internet collaboration tools, it is now feasible to crowd-source this digitization effort. The ODP emphasizes open science (so that all data are available immediately) while engaging the general public in real research. This demo will highlight several aspects of the project, including 1) coordinating efforts by professional paleontologists and interested amateurs; 2) data entry and verification; 3) blogging the research process; and 4) soliciting meaningful involvement in project design from participants of diverse backgrounds. Discuss here.
Explained here. Critiques in the comments are (mostly) valid, but for a first effort at using this kind of visualization technique, I'd say it's pretty impressive.
As you know you can see everyone who's registered for the conference, but I highlight 4-6 participants every day as this may be an easier way for you to digest the list. You can also look at the Program so see who is doing what.
Ian Oeschger is a writer, the editor of the hyper-local Wilminton NC journalism Grove Project, and an IBM information architect. He is also on Twitter.
Simon Frantz is the Senior Editor of the Nobel Prize website. And he tweets.
Earth's 24-h-rotation around its axis is mirrored in the circadian clock that resides within each of our cells, controlling expression of ~10% of all genes. The circadian clock is constructed as a negative feedback loop, in which clock proteins inhibit their own synthesis. During the last decade, a picture has emerged in which each cell is a self-sustained circadian oscillator that runs even without synchronizing cues. Here, we investigated state-of-the-art single-cell bioluminescence recordings of clock gene expression. It turns out that these time series are very well described by low-dimensional models, enabling us to extract descriptive parameters that characterize each cell. We find that different cell types do not differ much in their dynamics. However, different mutations in core clock genes yield different dynamic characteristics. Furthermore, we could not statistically reject the idea that the cells are in fact damped oscillators driven by noise. We thus declare the question of whether the circadian clock is a damped or self-sustained oscillator still unresolved. Further, we propose a way to resolve this question by examining the frequency-dependent response of single cells to periodic stimuli. We will then be in a better position to understand how cells coordinate and synchronize their circadian rhythms.
Light is an abundant signal that many organisms use to assess the status of their environment. Species from all kingdoms have evolved the capacity to sense and respond to wavelengths across the visible spectrum. Light has long been linked to disease (Figure 1); however, the mechanisms behind many of these observations are not well understood. Recently, a direct link has been established between specific protein photosensors and the ability to cause disease in both pathogenic bacteria and fungi [1]-[3]; thus, certain pathogens require these photosensors for full virulence. A role for photoperception is likely to emerge as a common theme in microbial pathogenesis.
One of the primary obstacles to understanding the computational underpinnings of biological vision is its sheer scale--the visual system is a massively parallel computer, comprised of billions of elements. While this scale has historically been beyond the reach of even the fastest super-computing systems, recent advances in commodity graphics processors (such as those found in the PlayStation 3 and high-end NVIDIA graphics cards) have made unprecedented computational resources broadly available. Here, we describe a high-throughput approach that harnesses the power of modern graphics hardware to search a vast space of large-scale, biologically inspired candidate models of the visual system. The best of these models, drawn from thousands of candidates, outperformed a variety of state-of-the-art vision systems across a range of object and face recognition tasks. We argue that these experiments point a new way forward, both in the creation of machine vision systems and in providing insights into the computational underpinnings of biological vision.
So. The time has come for me to get my kite flying, stretch out in the sun, kick off my shoes, and speak my piece. 'The days of struggle are over,' I should be able to say. 'I can look back now and tell myself I don't have a single regret.' But I do. Many.
Reminder: Deadline is December 1st at midnight EST!
Here are the submissions for OpenLab 2009 to date (under the fold). You can buy the 2006, 2007 and 2008 editions at Lulu.com. Please use the submission form to add more of your and other people's posts (remember that we are looking for original poems, art, cartoons and comics, as well as essays):
Make sure that the submitted posts are possible (and relatively easy) to convert into print. Posts that rely too much on video, audio, color photographs, copyrighted images, or multitudes of links just won't do.
As you know you can see everyone who's registered for the conference, but I highlight 4-6 participants every day as this may be an easier way for you to digest the list. You can also look at the Program so see who is doing what.
There are 19 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week - you go and look for your own favourites:
The circadian clock of the cyanobacterium Synechococcus elongatus can be reconstituted in vitro by three proteins, KaiA, KaiB and KaiC. Homo-hexameric KaiC displays kinase, phosphatase and ATPase activities; KaiA enhances KaiC phosphorylation and KaiB antagonizes KaiA. Phosphorylation and dephosphorylation of the two known sites in the C-terminal half of KaiC subunits, T432 and S431, follow a strict order (TS→pTS→pTpS→TpS→TS) over the daily cycle, the origin of which is not understood. To address this void and to analyze the roles of KaiC active site residues, in particular T426, we determined structures of single and double P-site mutants of S. elongatus KaiC. The conformations of the loop region harboring P-site residues T432 and S431 in the crystal structures of six KaiC mutant proteins exhibit subtle differences that result in various distances between Thr (or Ala/Asn/Glu) and Ser (or Ala/Asp) residues and the ATP γ-phosphate. T432 is phosphorylated first because it lies consistently closer to Pγ. The structures of the S431A and T432E/S431A mutants reveal phosphorylation at T426. The environments of the latter residue in the structures and functional data for T426 mutants in vitro and in vivo imply a role in dephosphorylation. We provide evidence for a third phosphorylation site in KaiC at T426. T426 and S431 are closely spaced and a KaiC subunit cannot carry phosphates at both sites simultaneously. Fewer subunits are phosphorylated at T426 in the two KaiC mutants compared to phosphorylated T432 and/or S431 residues in the structures of wt and other mutant KaiCs, suggesting that T426 phosphorylation may be labile. The structures combined with functional data for a host of KaiC mutant proteins help rationalize why S431 trails T432 in the loss of its phosphate and shed light on the mechanisms of the KaiC kinase, ATPase and phosphatase activities.
Traditional farming practices suggest that cultivation of a mixture of crop species in the same field through temporal and spatial management may be advantageous in boosting yields and preventing disease, but evidence from large-scale field testing is limited. Increasing crop diversity through intercropping addresses the problem of increasing land utilization and crop productivity. In collaboration with farmers and extension personnel, we tested intercropping of tobacco, maize, sugarcane, potato, wheat and broad bean - either by relay cropping or by mixing crop species based on differences in their heights, and practiced these patterns on 15,302 hectares in ten counties in Yunnan Province, China. The results of observation plots within these areas showed that some combinations increased crop yields for the same season between 33.2 and 84.7% and reached a land equivalent ratio (LER) of between 1.31 and 1.84. This approach can be easily applied in developing countries, which is crucial in face of dwindling arable land and increasing food demand.
Space limitation leads to competition between benthic, sessile organisms on coral reefs. As a primary example, reef-building corals are in direct contact with each other and many different species and functional groups of algae. Here we characterize interactions between three coral genera and three algal functional groups using a combination of hyperspectral imaging and oxygen microprofiling. We also performed in situ interaction transects to quantify the relative occurrence of these interaction on coral reefs. These studies were conducted in the Southern Line Islands, home to some of the most remote and near-pristine reefs in the world. Our goal was to determine if different types of coral-coral and coral-algal interactions were characterized by unique fine-scale physiological signatures. This is the first report using hyperspectral imaging for characterization of marine benthic organisms at the micron scale and proved to be a valuable tool for discriminating among different photosynthetic organisms. Consistent patterns emerged in physiology across different types of competitive interactions. In cases where corals were in direct contact with turf or macroalgae, there was a zone of hypoxia and altered pigmentation on the coral. In contrast, interaction zones between corals and crustose coralline algae (CCA) were not hypoxic and the coral tissue was consistent across the colony. Our results suggest that at least two main characteristic coral interaction phenotypes exist: 1) hypoxia and coral tissue disruption, seen with interactions between corals and fleshy turf and/or some species of macroalgae, and 2) no hypoxia or tissue disruption, seen with interactions between corals and some species of CCA. Hyperspectral imaging in combination with oxygen profiling provided useful information on competitive interactions between benthic reef organisms, and demonstrated that some turf and fleshy macroalgae can be a constant source of stress for corals, while CCA are not.
The impact of expanding civilization on the health of American indigenous societies has long been studied. Most studies have focused on infections and malnutrition that occurred when less complex societies were incorporated into more complex civilizations. The details of dietary change, however, have rarely been explored. Using the analysis of starch residues recovered from coprolites, here we evaluate the dietary adaptations of indigenous farmers in northern Chile's Atacama Desert during the time that the Inka Empire incorporated these communities into their economic system. This system has been described as "complementarity" because it involves interaction and trade in goods produced at different Andean elevations. We find that as local farming societies adapted to this new asymmetric system, a portion of their labor had to be given up to the Inka elite through a corvée tax system for maize production. In return, the Inka system of complementarity introduced previously rare foods from the Andean highlands into local economies. These changes caused a disruption of traditional communities as they instituted a state-level economic system on local farmers. Combined with previously published infection information for the same populations under Inka rule, the data suggest that there may have been a dual health impact from disruption of nutrition and introduction of crowd disease.
There comes a time when for every addition of knowledge you forget something that you knew before. It is of the highest importance, therefore, not to have useless facts elbowing out the useful ones.
Reminder: Deadline is December 1st at midnight EST!
Here are the submissions for OpenLab 2009 to date (under the fold). You can buy the 2006, 2007 and 2008 editions at Lulu.com. Please use the submission form to add more of your and other people's posts (remember that we are looking for original poems, art, cartoons and comics, as well as essays):
Make sure that the submitted posts are possible (and relatively easy) to convert into print. Posts that rely too much on video, audio, color photographs, copyrighted images, or multitudes of links just won't do.
As you know you can see everyone who's registered for the conference, but I highlight 4-6 participants every day as this may be an easier way for you to digest the list. You can also look at the Program so see who is doing what.
Eric Michael Johnson is an evolutionary anthropologist, a historian of science and a blogger at The Primate Diaries. He is also on Twitter. At the conference, Eric will co-moderate the session An Open History of Science.
There are 25 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week - you go and look for your own favourites:
The extinct Huia (Heteralocha acutirostris) of New Zealand represents the most extreme example of beak dimorphism known in birds. We used a combination of nuclear genotyping methods, molecular sexing, and morphometric analyses of museum specimens collected in the late 19th and early 20th centuries to quantify the sexual dimorphism and population structure of this extraordinary species. We report that the classical description of Huia as having distinctive sex-linked morphologies is not universally correct. Four Huia, sexed as females had short beaks and, on this basis, were indistinguishable from males. Hence, we suggest it is likely that Huia males and females were indistinguishable as juveniles and that the well-known beak dimorphism is the result of differential beak growth rates in males and females. Furthermore, we tested the prediction that the social organisation and limited powers of flight of Huia resulted in high levels of population genetic structure. Using a suite of microsatellite DNA loci, we report high levels of genetic diversity in Huia, and we detected no significant population genetic structure. In addition, using mitochondrial hypervariable region sequences, and likely mutation rates and generation times, we estimated that the census population size of Huia was moderately high. We conclude that the social organization and limited powers of flight did not result in a highly structured population.
KaiC, a central clock protein in cyanobacteria, undergoes circadian oscillations between hypophosphorylated and hyperphosphorylated forms in vivo and in vitro. Structural analyses of KaiC crystals have identified threonine and serine residues in KaiC at three residues (T426, S431, and T432) as potential sites at which KaiC is phosphorylated; mutation of any of these three sites to alanine abolishes rhythmicity, revealing an essential clock role for each residue separately and for KaiC phosphorylation in general. Mass spectrometry studies confirmed that the S431 and T432 residues are key phosphorylation sites, however, the role of the threonine residue at position 426 was not clear from the mass spectrometry measurements. Mutational approaches and biochemical analyses of KaiC support a key role for T426 in control of the KaiC phosphorylation status in vivo and in vitro and demonstrates that alternative amino acids at residue 426 dramatically affect KaiC's properties in vivo and in vitro, especially genetic dominance/recessive relationships, KaiC dephosphorylation, and the formation of complexes of KaiC with KaiA and KaiB. These mutations alter key circadian properties, including period, amplitude, robustness, and temperature compensation. Crystallographic analyses indicate that the T426 site is phosphorylatible under some conditions, and in vitro phosphorylation assays of KaiC demonstrate labile phosphorylation of KaiC when the primary S431 and T432 sites are blocked. T426 is a crucial site that regulates KaiC phosphorylation status in vivo and in vitro and these studies underscore the importance of KaiC phosphorylation status in the essential cyanobacterial circadian functions. The regulatory roles of these phosphorylation sites-including T426-within KaiC enhance our understanding of the molecular mechanism underlying circadian rhythm generation in cyanobacteria.
Many coral reef organisms are photosynthetic or have evolved in tight symbiosis with photosynthetic symbionts. As such, the tissues of reef organisms are often exposed to intense solar radiation in clear tropical waters and have adapted to trap and harness photosynthetically active radiation (PAR). High levels of ultraviolet radiation (UVR) associated with sunlight, however, represent a potential problem in terms of tissue damage. By measuring UVR and PAR reflectance from intact and ground bare coral skeletons we show that the property of calcium carbonate skeletons to absorb downwelling UVR to a significant extent, while reflecting PAR back to the overlying tissue, has biological advantages. We placed cnidarians on top of bare skeletons and a UVR reflective substrate and showed that under ambient UVR levels, UVR transmitted through the tissues of cnidarians placed on top of bare skeletons were four times lower compared to their counterparts placed on a UVR reflective white substrate. In accordance with the lower levels of UVR measured in cnidarians on top of coral skeletons, a similar drop in UVR damage to their DNA was detected. The skeletons emitted absorbed UVR as yellow fluorescence, which allows for safe dissipation of the otherwise harmful radiation. Our study presents a novel defensive role for coral skeletons and reveals that the strong UVR absorbance by the skeleton can contribute to the ability of corals, and potentially other calcifiers, to thrive under UVR levels that are detrimental to most marine life.
Food waste contributes to excess consumption of freshwater and fossil fuels which, along with methane and CO2 emissions from decomposing food, impacts global climate change. Here, we calculate the energy content of nationwide food waste from the difference between the US food supply and the food consumed by the population. The latter was estimated using a validated mathematical model of metabolism relating body weight to the amount of food eaten. We found that US per capita food waste has progressively increased by ~50% since 1974 reaching more than 1400 kcal per person per day or 150 trillion kcal per year. Food waste now accounts for more than one quarter of the total freshwater consumption and ~300 million barrels of oil per year.
Elucidating geographic locations from where migratory birds are recruited into adult breeding populations is a fundamental but largely elusive goal in conservation biology. This is especially true for species that breed in remote northern areas where field-based demographic assessments are logistically challenging. Here we used hydrogen isotopes (δD) to determine natal origins of migrating hatch-year lesser scaup (Aythya affinis) harvested by hunters in the United States from all North American flyways during the hunting seasons of 1999-2000 (n = 412) and 2000-2001 (n = 455). We combined geospatial, observational, and analytical data sources, including known scaup breeding range, δD values of feathers from juveniles at natal sites, models of δD for growing-season precipitation, and scaup band-recovery data to generate probabilistic natal origin landscapes for individual scaup. We then used Monte Carlo integration to model assignment uncertainty from among individual δD variance estimates from birds of known molt origin and also from band-return data summarized at the flyway level. We compared the distribution of scaup natal origin with the distribution of breeding population counts obtained from systematic long-term surveys. Our analysis revealed that the proportion of young scaup produced in the northern (above 60°N) versus the southern boreal and Prairie-Parkland region was inversely related to the proportions of breeding adults using these regions, suggesting that despite having a higher relative abundance of breeding adults, the northern boreal region was less productive for scaup recruitment into the harvest than more southern biomes. Our approach for evaluating population declines of migratory birds (particularly game birds) synthesizes all available distributional data and exploits the advantages of intrinsic isotopic markers that link individuals to geography.
Despite the ubiquity of raptors in terrestrial ecosystems, many aspects of their predatory behaviour remain poorly understood. Surprisingly little is known about the morphology of raptor talons and how they are employed during feeding behaviour. Talon size variation among digits can be used to distinguish families of raptors and is related to different techniques of prey restraint and immobilisation. The hypertrophied talons on digits (D) I and II in Accipitridae have evolved primarily to restrain large struggling prey while they are immobilised by dismemberment. Falconidae have only modest talons on each digit and only slightly enlarged D-I and II. For immobilisation, Falconini rely more strongly on strike impact and breaking the necks of their prey, having evolved a 'tooth' on the beak to aid in doing so. Pandionidae have enlarged, highly recurved talons on each digit, an adaptation for piscivory, convergently seen to a lesser extent in fishing eagles. Strigiformes bear enlarged talons with comparatively low curvature on each digit, part of a suite of adaptations to increase constriction efficiency by maximising grip strength, indicative of specialisation on small prey. Restraint and immobilisation strategy change as prey increase in size. Small prey are restrained by containment within the foot and immobilised by constriction and beak attacks. Large prey are restrained by pinning under the bodyweight of the raptor, maintaining grip with the talons, and immobilised by dismemberment (Accipitridae), or severing the spinal cord (Falconini). Within all raptors, physical attributes of the feet trade off against each other to attain great strength, but it is the variable means by which this is achieved that distinguishes them ecologically. Our findings show that interdigital talon morphology varies consistently among raptor families, and that this is directly correlative with variation in their typical prey capture and restraint strategy.
Observing competitive games such as sports is a pervasive entertainment among humans. The inclination to watch others play may be based on our social-cognitive ability to understand the internal states of others. The mirror neuron system, which is activated when a subject observes the actions of others, as well as when they perform the same action themselves, seems to play a crucial role in this process. Our previous study showed that activity of the mirror neuron system was modulated by the outcome of the subject's favored player during observation of a simple competitive game (rock-paper-scissors). However, whether the mirror neuron system responds similarly in a more complex and naturalistic sports game has not yet been fully investigated. In the present study, we measured the activity of motor areas when the subjects, who were amateur baseball field players (non-pitchers), watched short movie clips of scenes in professional baseball games. The subjects were instructed to support either a batter or a pitcher when observing the movie clip. The results showed that activity in the motor area exhibited a strong interaction between the subject's supported side (batter or pitcher) and the outcome (a hit or an out). When the subject supported the batter, motor area activity was significantly higher when the batter made an out than when he made a hit. However, such modulation was not apparent when the subject supported the pitcher. This result indicates that mirror neuron system activity is modulated by the outcome for a particular player in a competitive game even when observing a complex and naturalistic sports game. We suggest that our inclination to watch competitive games is facilitated by this characteristic of the mirror neuron system.
Traders in the financial world are assessed by the amount of money they make and, increasingly, by the amount of money they make per unit of risk taken, a measure known as the Sharpe Ratio. Little is known about the average Sharpe Ratio among traders, but the Efficient Market Hypothesis suggests that traders, like asset managers, should not outperform the broad market. Here we report the findings of a study conducted in the City of London which shows that a population of experienced traders attain Sharpe Ratios significantly higher than the broad market. To explain this anomaly we examine a surrogate marker of prenatal androgen exposure, the second-to-fourth finger length ratio (2D:4D), which has previously been identified as predicting a trader's long term profitability. We find that it predicts the amount of risk taken by traders but not their Sharpe Ratios. We do, however, find that the traders' Sharpe Ratios increase markedly with the number of years they have traded, a result suggesting that learning plays a role in increasing the returns of traders. Our findings present anomalous data for the Efficient Markets Hypothesis.
Approximately 10 million Americans enter jails annually. The Centers for Disease Control and Prevention now recommends routine opt-out HIV testing in these settings. The logistics for performing routine opt-out HIV testing within jails, however, remain controversial. The objective of this study was to evaluate the optimal time to routinely HIV test newly incarcerated jail detainees using an opt-out strategy. This prospective, controlled trial of routine opt-out HIV testing was conducted among 298 newly incarcerated male inmates in an urban men's jail in New Haven, Connecticut. 298 sequential entrants to the men's jail over a three week period in March and April 2008 were assigned to be offered routine opt-out HIV testing at one of three points after incarceration: immediate (same day, n = 103), early (next day, n = 98), or delayed (7 days, n = 97). The primary outcome was the proportion of men in each group consenting to testing. Routine opt-out HIV testing was significantly higher for the early (53%: AOR = 2.6; 95% CI = 1.5 to 4.7) and immediate (45%: AOR = 2.3; 95% CI = 1.3 to 4.0) testing groups compared to the delayed (33%) testing group. The immediate and early testing groups, however, did not significantly differ (p = 0.67). In multivariate analyses, factors significantly associated with routine opt-out HIV testing were assignment to the 'early' testing group (p = 0.0003) and low (bond ≥$5,000, immigration or federal charges or pre-sentencing >30 days) likelihood of early release (p = 0.04). Two subjects received preliminary positive results and one of them was subsequently confirmed HIV seropositive. In this men's jail where attrition was high, routine opt-out HIV testing was not only feasible, but resulted in the highest rates of HIV testing when performed within 24 hours of incarceration.
Ten million Americans enter jails annually. The objective was to evaluate new CDC guidelines for routine opt-out HIV testing and examine the optimal time to implement routine opt-out HIV testing among newly incarcerated jail detainees. This prospective, controlled trial of routine opt-out HIV testing was conducted among 323 newly incarcerated female inmates in Connecticut's only women's jail. 323 sequential entrants to the women's jail over a five week period in August and September 2007 were assigned to be offered routine opt-out HIV testing at one of three points after incarceration: immediate (same day, n = 108), early (next day, n = 108), or delayed (7 days, n = 107). The primary outcome was the proportion of women in each group consenting to testing. Routine opt-out HIV testing was significantly highest (73%) among the early testing group compared to 55% for immediate and 50% for 7 days post-entry groups. Other factors significantly (p = 0.01) associated with being HIV tested were younger age and low likelihood of early release from jail based on bond value or type of charge for which women were arrested. In this correctional facility, routine opt-out HIV testing in a jail setting was feasible, with highest rates of testing if performed the day after incarceration. Lower testing rates were seen with immediate testing, where there is a high prevalence of inability or unwillingness to test, and with delayed testing, where attrition from jail increases with each passing day.
This is a predictive validity study examining the extent to which developmental vulnerability at kindergarten entry (as measured by the Early Development Instrument, EDI) is associated with children's basic skills in 4th grade (as measured by the Foundation Skills Assessment, FSA). Relative risk analysis was performed on a large database linking individual-level EDI ratings to the scores the same children obtained on a provincial assessment of academic skills (FSA - Foundation Skills Assessment) four years later. We found that early vulnerability in kindergarten is associated with the basic skills that underlie populations of children's academic achievement in reading, writing and math, indicating that the Early Development Instrument permits to predict achievement-related skills four years in advance. The EDI can be used to predict children's educational trends at the population level and can help select early prevention and intervention programs targeting pre-school populations at minimum cost.
Last couple of weeks months were awfully busy, on many fronts, not least finalizing the ScienceOnline2010 program, herding cats almost 100 moderators/presenters to do various stuff (e.g., respond to my e-mails) in a timely manner, and making sure that registration goes smoothly. This is also the time of year when activation energy for doing anything except going to bed to hide under the covers is very high for people suffering from SAD. Thus, you did not see many 'original' posts here lately, I know.
But, it's not that I have been totally idle. Apart from teaching my BIO101 lab again, I also went to several science-related events in the Triangle over the past two months. I feel like I should blog about each one of them separately, at length and with nuance, as this hangs over my neck like the Sword of Damocles - I feel I should not blog about anything else until all of these event reports are out of the way.
So, in a compromise solution, instead of a bunch of long separate posts, I will collect all the brief reports from all the events here, in a single post, get that over with and mentally free myself to blog about other stuff soon.
Lisa Sanders at UNC
Lisa Sanders is a physician and a professor of medicine, but you probably heard of her in a different context: Lisa writes the Diagnosis column in The New York Times, has recently published a book Every Patient Tells a Story, and has inspired and acts as the medical adviser to the TV show House (of which I heard, not being a TV watcher, at the beginning of her talk).
Lisa Sanders came to the Triangle last month and gave talks at Duke and UNC. Bride of Coturnix and I went to the UNC talk which filled a large auditorium. Her book is being read by all the UNC medical students who will then discuss the book in smaller groups.
The process of diagnosis has three steps: interview, physical exam and laboratory tests.
Laboratory tests have become more and more dominant as the preferred part of the diagnosis process, for a number of (cultural) reasons:
First, they are the quickest, thus save the physician time (others do the work).
Second, unlike interviews that seem subjective, or physical exams that look medieval, lab tests look like ScienceTM! - there are numbers there. And you can't argue against numbers, can you? This works great on the background of lack of statistical sophistication (or outright innumeracy) on the part of both physicians and patients. No arguing. No second opinions. The process moves on smoothly for everyone. Except, the numbers cannot be trusted as much they usually are.
Third, a number is not an opinion, thus it is a safeguard against lawsuits. It saves physician's asses in such cases.
Both the frenzy and the (perceived) lack of time and the fear of lawsuits would be diminished if we had a real healthcare reform (not the compromise of a compromise of a compromise bill that is brewing in the US Senate right now, but an actual reform) in which the physicians could get their authority and trust back and be able to practice their art and craft and science with some degree of freedom. In a system in which insurance companies determine how care is done, physicians are just technicians and cannot earn authority and trust.
So, with everyone jumping onto lab tests, the art of interview and the art of physical examination are slowly dying out. They are not even taught in some medical schools any more. Where they are taught, as soon as newly minted physicans are on their own they join the medical culture that frowns upon these two steps of the diagnostic process.
Yet, Dr.Sanders showed data from two studies (done in different countries by different people in different years), both providing almost exactly the same results. In about 75-80% of the cases (physician encountering a new patient for the first time), the physician comes up with a correct diagnosis after the interview. In about 10-12% of the cases, the doctor has to correct her/himself after the physical exam in order to arrive at the correct diagnosis. And in only the remaining 10-12% or so cases did the lab tests provide information that forced the physician to change one's mind and come up with the correct diagnosis. In 8 out of 10 cases, the interview was sufficient!
When asked why they are shunning the interviews, physicians respond that they have no time - the system is forcing them to see too many patients per day. A study shows that physicians interrupt patients' stories abruptly, very soon, sometimes as early as 3 seconds into the interview. Yet, in another study, when doctors were asked specifically not to interrupt, the interviews lasted only one minute longer. Just one minute! Thus interruption does not really save any time - it's an illusion.
But what is more important is that the interruption itself means something. First, it means that the physician is not really listening. Second, it tells the patient that the doctor is not listening. By relaxing for that extra minute and actively listening to the patient, not just fishing for diagnostically important information in the account but also listening to hear how the patient perceives him/herself, and how that perception is altered by the illness, the physician gains a better understanding of the patient, can probably come up with a better diagnosis and, most importantly, gains trust with the patient. That trust is very important later, when the physician needs to rely on the patients to be disciplined about the treatment. The interruption loses that trust, something that smooth-talking medical quacks are quick to jump on, offering to listen even if their treatments are completely bogus.
What a patient does during the interview is story-telling. A physician needs to be trained to listen to and understand such stories - to glean how the change in health status affects the self-confidence, self-view and self-worth of the patient, how it changes one's life-plans and ambitions, what fears it brings, what difficult adjustments in lifestyle it requires. To see the patient as a person, not just a disease.
And then, the story-telling does not end with the interview. The physicians and nurses need to communicate with each other about the patient and that also entails, when done right, story-telling (which need not be spoken, it can be in the chart). Finally, the healthcare providers need to know how to tell the story back to the patient, both to convey the diagnosis and to gain the trust needed for the patient to accept and follow through with the treatment. Quick recitatiton of code-numbers and Latin words just won't do.
So Lisa Sanders, with her book, her column, her advising of House MD and her speaking tour, tries to teach the importance of the interview and the physical exam, the art of listening and storytelling. I am glad that UNC is taking her seriously.
The next day, a bunch of us met with Dr.Sanders at the West End Wine Bar in Durham. It was great fun to talk to her in an informal setting and to ask questions that I did not dare ask at the public talk in front of hundreds of med school professors and students and something like the entire nursing school of UNC. After all, my only perspective on medicine is from the position of a patient (and a reader of some med-blogs) so I learned a lot, yet was aware how little I actually know about medical training and practice. Anton organized that meet-up with the local science communicators and wrote his summary of the week's events on his blog:
Steven Churchill at Sigma Xi
Steven Churchill is a professor of Evolutionary Anthropology at Duke University. His focus is on the role of projectile weapons in the evolution of humans. Dr.Churchill gave a talk at Sigma Xi as a part of their Pizza Lunch monthly series.
What is a projectile weapon? It is something that can be thrown far away - more than just a couple of meters - and with sufficient power to seriously injure or kill a large animal. A non-projectile weapon, even if it can be thrown with force to a shorter distance of a couple of meters, requires either ambush hunting or chasing the prey into a corner or a bog where it can be approached and stabbed from a close distance. A projectile weapon allows hunters to hunt out in the open, perhaps just hiding in the tall grass. Thus two types of weaponry target different kinds of prey.
But inventing projectile weapons requires refinement in technical skills of making them, technical skills in throwing them, and changes in anatomy to make projectile weapons effective. And once invented, projectile weapons have novel ecological impacts, including impacts on further cultural evolution of humans.
This is what Dr.Churchill is studying. He is focusing on Europe, the invention of projectile weapons by modern ("Cro-Magnon") humans and lack of such invention in Neanderthals, how that impacted the ecological relationship between the two species, and how that contributed to Neanderthal extinction as well as extinction (through competitive exclusion, as well as direct competition by killing) of all the large European carnivores except wolves.
In the talk, Dr.Churchill surveyed several different aspects of his research. He is approaching the question from several different angles. One is the study of spear tips in the archaeological record - their shape and size, the weight, the aerodynamics of the shape, etc. all tell something about their use as either close-contact or projectile weapons. Some (rare) spear handles and spear-throwers tell their own stories.
Then there is the fossil record of humans, Neanderthals and other large carnivores that show numbers and geographical distributions, migrations and dates of extinctions.
Next, there are anatomical cues - skeleton is malleable during development and bones in the upper arm develop differently in cultures that use contact weapons versus those that use projectile weapons as the stabbing technique is different from the throwing technique - throwers have different torsion angles in the humerus and also the humerus of one arm gets thicker than that of the other arm - this pattern is found in humans, but not in Neanderthals.
Finally, the general shape of Neanderthals would make them strong stabbers but poor throwers, so even if they tried throwing (perhaps by seeing the spears used that way by modern humans) they would not have been effective hunters with that technique.
Then, there are wounds in the bones of some fossil humans and Neanderthals. By conducting an experiment - throwing spears into pig carcasses at various speeds, powers and distances (yes, throwing done by a machine) and analyzing the effects on bones - Churchill and his students could conclude that the wounds in the fossil bones were indeed the result of projectile weapons thrown from a distance.
The talk was, as is usually the case on these occasions, a quick survey of various studies. I did not read all the papers by him or his competitors, so I cannot write anything from a position of my own expertise. But my feeling is this:
Each piece of evidence he showed is weak on its own, but put together they make a strong case. And the strength is not purely additive, i.e., in the sense that more data is stronger than fewer data. The strength comes from consilience. Let me try to explain how that works.
Let's call his preferred hypothesis 'Hypothesis A'. One piece of evidence he shows is consistent with Hypothesis A, and weakens (or eliminates) an alternative Hypothesis B, but is also strongly vulnerable to alternative Hypothesis C. Another piece of evidence is consistent with his Hypothesis A, and weakens an alternative Hypothesis C, but is also strongly vulnerable to alternative Hypothesis D. Yet another piece of evidence is consistent with his Hypothesis A, and weakens an alternative Hypothesis D, but is also strongly vulnerable to alternative Hypothesis B. When you look at all of his evidence together, all of it is consistent with Hypothesis A and all alternatives look weak. Thus with all pieces being individually weak, the whole edifice still looks very powerful.
Now, to make clear, Dr.Churchill pointed out several times that the research he focuses on, his Hypothesis A, is not the one and only explanation for the extinction of Neanderthals (and other large predators). He just asserts that it is an important component of the process that led to this result and perhaps a more important component than some other people in the field are ready to admit. Of course, that's how science works: different people focus on different aspects of a problem, and the strength of each person's data will determine how the whole picture is built in the end.
This was definitely an interesting talk on a topic I never thought about before. DeLene was also there and wrote her thoughts about the lecture on her blog Wild Muse as well as on the Science In The Triangle blog.
RTI Fellows Symposium: Integrating Basic and Applied Research
This was a two-day event at the University of North Carolina's Friday Center in Chapel Hill. This was also the first time I saw the Friday Center from within and I was looking at it with the eyes of a conference organizer. It has a Goldilocks quality to it: not so pleasant, intimate and science-themed as Sigma Xi, and not as big, cold and corporate as the Raleigh Convention Center. Just the right size and feel. But expensive as hell - Sigma Xi has been good to us over the years, not sure if we could negotiate a similar deal with Friday.....though we have definitely grown and a 420-seat main conference room at Friday Center looks good.
I could attend only the Monday morning portion of the meeting, but Sabine Vollmer was at the Symposium for the whole thing and wrote two blogs posts about the rest of the program here and here with a lot of details.
There were four broad themes entertained by the symposium: Personalized Medicine, Behavioral Neuroscience of Alcoholism, Global Climate Change and Education Opportunity and Achievement. Each of the themes had its own breakout session later, but Monday morning was reserved for Keynote Speakers, one on each of the four topics, each of interest to me in one way or another.
Let me first dispose of the things I did not like about the conference before I get into things I liked.
Over the past few years, most of the conferences I go to are informal, unconference or unconference-like events: from Scifoo in Mountain View, to Science FEST in Trieste, to ConvergeSouth in Greensboro, to our own ScienceOnline meetings. Even the 'real' science meeting I like to go to, the SRBR meeting, is very relaxed and informal - shorts-and-Hawaiian-shirt-clad scientists giving funny and entertaining talks about their new findings in my own field, with internal jokes, calling out friends in the audience and occasional hackling joke from the room (OK, OK, I overstate - folks are mostly nice and polite, especially when the talk is given by someone younger, e.g, a properly dressed graduate student, waiting in attentive silence until the end and then asking proper questions afterwards, but still, the general atmosphere is friendly and relaxed).
I realize of course that different conferences require different setup and different levels of formality. Not everything is a Bar Camp. While I was personally uncomfortable wearing my suit-and-tie costume at the IASP meeting, I understood that this was a business meeting in a business venue with businessmen (and a handful of businesswomen) in business attire talking about business.
But this one, I think, was a mismatch. All (or almost all) speakers were scientists talking about science. Almost everyone in the audience were scientists. For this kind of meeting, the organization was far too formal. And not just in pomp and ceremony and dress-code. For example, if you look at the abstracts, they don't really say anything about the topic of the talk - they go in great detail about the speaker, including all the past and present appointments, awards and honorary degrees. This indicates that the organizers were more interested in the power hierarchy (i.e., 'look at VIPs we managed to get here to talk') instead of the substance of what they are saying. It felt more like a big corporate show-off than a conference meant for an exchange of ideas.
Then, there was no time designated for Question & Answer periods after the talks. I wanted to ask questions, but there was just no mechanism for doing so. I understand there were panels afterwards, but even those were built strangely - with panelists, after each gave a separate talk, sitting at a table on a podium above the audience, physically looking down at the audience, thus psychologically inhibiting all but the bravest from actually speaking up. I do not know how it went, but I doubt it was a free-wheeling discussion.
Then, the talks. Two speakers actually read their talks. Arrrgh! Yawn (and I was FULL of caffeine).
Others were much better. Howard McLeod gave a good, clear introduction into personal genomics and personal medicine, its pros and cons. Robert Jackson from Duke provided a good summary of the current state of science of climate change.
Ronald Dahl talked about adolescent brain development (something I am very interested in, both professionally and as a father of two adolescents), especially the lengthening of the period between onset of puberty which arrives earlier and earlier (the timing of which is not matched by an earlier development of other brain functions, including self-control) and the delay of societally approved age for onset of sexual activity (including marriage). Thus the duration of the period during which adolescents are sexually mature (but not entirely emotionally mature) but discouraged from sexual activity is getting longer and longer - which is an obvious problem. Couple that with the tendency of adolescents to be unable to resist, despite personal fear, engaging in risky behaviors, problems like teen alcoholism and traffic accidents are on the rise.
Lunch Keynote Speaker, Ralph Tarter, was the biggest dissapointment. His talk about bridging the Two Cultures and lessons from Hollywood was surprising for its naivete easily detectable by anyone who's been reading science blogs for more than a year or so (including Framing Wars, response to Sizzle and response to Unscientific America, along with bloggers who routinely write about history of science). It was infused with nostalgia for good old days when scientists and poets drank wine and talked together (ehm, scientists and poets at the time were the one and the same people - that was Victorian era when gentlemen of means could afford to indulge themselves in such pastimes as philosophy, natural history and poetry and meeting their like-minded buddies at the pub). Science today is a very different business, specialized, expensive, profesionalized and rightly so. That's progress.
The worst part was the lunch talk was the last point - a very erroneous analogy between peer-review of grants and movie reviews. First error: grants are reviewed before they are funded - movies are reviewed after they are funded. Second, as much as the grant review is prone to error, it is still done by well-meaning teams of scientists who are at least trying to evaluate the proposals according to their merits. Yes, outlandish proposals have a harder time than bandwagon stuff or conservative approaches, but it is at least attempted to be done fairly. Which movie gets funded is totally up to whims of movie moguls and producers. I bet even smaller percentage of submitted movie scripts gets actually made into movies than a proportion of grant proposals that gets funded. And while grant reviewers may look at the past publishing records of the grant submitters, the movie magnates are not in any way swayed by the statistics of positive or negative views of particular actors by movie critics in the media.
The highlight of the day was the talk by James Evans. I know Jim well, but I have never seen him speak before. And he blew me away. He knew that all the other speakers on the Personalized Medicine topics will be over-optimistic, so he took it on himself to provide a counter-view, a summary of cautionary notes backed up by data and a nice dose of humor. It was a very energetic and fun talk that explained very clearly what claims by personal genomics companies really mean, why they are so seductive if you don't stop to think about them, and how they stack up against reality.
NESCent panel on intersection of public policy, economics, & evolution
NESCent Catalysis Meeting, coorganized by the Evolution Institute was on November 13-15, 2009 and several of the participants remained another day and came to NESCent on the 16th to report on the meeting in a form of a panel. The meeting and the panel were organized by David Sloan Wilson, professor of evolution at Binghamton University and one of my newest SciBlings. The other panelists were Dennis Embry, John Gowdy, Douglas Kenrick, Joel Peck, Harvey Whitehouse and Peter Turchin.
The main idea of the meeting is that evolutionary theory has something to offer in the realm of understanding human societies and thus shaping policies governing aspects of human activity. In the domain of economics, for example, it appears that the classical economics (i.e., the Chicago School) is unbeatable in the corridors of power. Yet, it is essentially faulty and this has been shown many times, including by numerous Nobel Prize winners in Economics. The idea that humans are rational (and perfectly informed) economic players is just plain wrong. Yet our economic policy is built upon that error. Perhaps developing and using models from evolutionary theory can finally bring the well-past-due overturn of the faulty economics and become the basis for smart, modern economic policies. The work is just beginning.
Perhaps the insights from the study of social and eusocial animals, mainly insects, can inform the discussion about social behavior of humans. How do simple rules for simple brains result in complex behaviors of, for example, bee swarms? Perhaps if we used such simple rules, instead of relying on every individual human being highly intelligent, impartial and rational, we can devise policies that will actually work, in various domains of human activity.
Taking into account multi-level selection models of evolution one can start understanding the differences between small-group societies (e.g, in rural areas) and large-group societies (e.g., in large cities), why those result in diefferent behaviors of individual humans living there, and why the differences between the two types of groups often lead to civil wars (often wars we usually do not see or describe as civil wars due to our own myopia, not realizing that a war between two adjacent regions may, in fact, be a war between the city and the country "mentality" - something quite obviously applicable to the US red vs. blue states, really small-town conservatism vs. big-city liberalism). Why imposing large-group organization (i.e., a President and a Parliament, i.e., a 'centralized government' of a unified country) may not work in a country like Afghanistan in which the society was always organized via local kin-and-friend networks - evolutionary theory can open our eyes on such questions.
This group of people, coming from a variety of backgrounds including history, anthropology, ecology, economics, psychology, political science, ethology and evolutionary biology, will try to tackle these and similar questions over the years to come.
Interestingly, the meeting was apparently an Unconference (though they have never heard of the term before), with discussions starting some months before the event (I presume online), leading to the choices of topics actually discussed in sessions which were free-style discussions, not speeches. One of the panelists noted that interdisciplinary meetings are usually excercises in misunderstanding, as each participant brings in different language and different axioms, but not this meeting - people actually made an effort, in advance, to study and learn other people's perspectives before encountering them in the sessions in real life. This made the meeting, judging from the enthusiasm of all panelists, a resounding success.
This was the first time I ever visited NESCent (though I was excited when I first heard about its founding five years ago) and it was really nice to see Craig McClain and Robin Ann Smith again, as well as to meet, for the first time in real life, John Logsdon who blogs on Sex, Genes and Evolution and has come to NESCent for a nine-year sabbatical.
Solid Waste Management Vendor Fair at the RTP Headquarters
I got to see this almost by accident. I was going to the RTP headquarters to talk to them about their new blog and, for the price of free pizza, wondered around the exhibit and saw a brief talk about the ways North Carolina is doing recycling solid waste, why that is a good thing, and what are the prospect for the future. But I will let Cara Rousseau give you more details, in a post on the new RTP blog.
SCONC celebration of the Origin of Species 150-year anniversary at NESCent
Just a couple of days after my first ever visit to NESCent, I found myself there again. The occasion, the anniversary of the publication of the Origin Of Species (though officially today), was a good excuse for SCONC to have its monthly meeting at NESCent.
Robin Smith welcomed us all with a piece of great news - the funding for NESCent was extended for another five years! Then, while we were enjoying some delicious food, we were treated to three interesting presentations by current NESCent post-docs: Julie Meachen-Samuels talking about Smilodon, how it hunted differently than modern Big Cats and what it means for our understanding of palaeo-ecology and evolution, Trina Roberts about the diversity and biogeography of tree shrews (and how to get DNA from museum skeletal specimens!), and Eric Schuettpelz about the way ferns radiated into many species with the appearance of forests of (flowering) trees by occupying a new niche - living on the tree trunks as epiphytes, in the shade.
I found myself thinking about parallels between the Smilodon presentation and the one on projectile weapons I heard a couple of weeks before. Neanderthals uses stabbing close-contact weapons (and are now extinct) while modern humans used projectile weapons, thus being able to hunt different kinds of prey (and are now extant). Similarly, most Big Cats today hunt by giving chase to their prey and then killing it with their long canine teeth, often having to hold the teeth clenched in the trachea for several minutes until the victim dies. But Smilodons (the saber-tooth cats) had to hunt differently - from an ambush, presumably in thick forests and not out in the open country. They overpowered their prey using the weight and strength of their forelimbs and only at the end finished the completely immobilized victim with a quick slice with their canines. If they tried to keep their teeth inside still struggling large animals for more than a moment, their long but thin canines would break. In some ways, the Smilodon hunting technique is analogous to using close-quarters weapons, while the techniques of modern Big Cats is more analogous to hunting with projectile weapons (with themselves being "projectiles"). With such a massive body, with hindquarters so much smaller than the front half of the animal, and with no tail they could use for balance, saber-tooth cats could not run fast enough and long enough to be "projectiles". Perhaps that's why they, like Neanderthals, are now all dead.
Reminder: Deadline is December 1st at midnight EST!
Here are the submissions for OpenLab 2009 to date (under the fold). You can buy the 2006, 2007 and 2008 editions at Lulu.com. Please use the submission form to add more of your and other people's posts (remember that we are looking for original poems, art, cartoons and comics, as well as essays):
Make sure that the submitted posts are possible (and relatively easy) to convert into print. Posts that rely too much on video, audio, color photographs, copyrighted images, or multitudes of links just won't do.
As you know you can see everyone who's registered for the conference, but I highlight 4-6 participants every day as this may be an easier way for you to digest the list. You can also look at the Program so see who is doing what.
Dennis Meredith is a freelance writer and consultant, with a long career in science communication. He is the creator and developer of EurekAlert and blogs on Research Explainer
There are 39 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week - you go and look for your own favourites:
Species Distribution Models (SDMs) aim on the characterization of a species' ecological niche and project it into geographic space. The result is a map of the species' potential distribution, which is, for instance, helpful to predict the capability of alien invasive species. With regard to alien invasive species, recently several authors observed a mismatch between potential distributions of native and invasive ranges derived from SDMs and, as an explanation, ecological niche shift during biological invasion has been suggested. We studied the physiologically well known Slider turtle from North America which today is widely distributed over the globe and address the issue of ecological niche shift versus choice of ecological predictors used for model building, i.e., by deriving SDMs using multiple sets of climatic predictor. In one SDM, predictors were used aiming to mirror the physiological limits of the Slider turtle. It was compared to numerous other models based on various sets of ecological predictors or predictors aiming at comprehensiveness. The SDM focusing on the study species' physiological limits depicts the target species' worldwide potential distribution better than any of the other approaches. These results suggest that a natural history-driven understanding is crucial in developing statistical models of ecological niches (as SDMs) while "comprehensive" or "standard" sets of ecological predictors may be of limited use.
Understanding the behavior of birds in agricultural habitats can be the first step in evaluating the conservation implications of birds' use of landscapes shaped by modern agriculture. The existence and magnitude of risk from agricultural practices and the quality of resources agricultural lands provide will be determined largely by how birds use these habitats. Buff-breasted Sandpipers (Tryngites subruficollis) are a species of conservation concern. During spring migration large numbers of Buff-breasted Sandpipers stopover in row crop fields in the Rainwater Basin region of Nebraska. We used behavioral observations as a first step in evaluating how Buff-breasted Sandpipers use crop fields during migratory stopover. We measured behavior during migratory stopover using scan and focal individual sampling to determine how birds were using crop fields. Foraging was the most frequent behavior observed, but the intensity of foraging changed over the course of the day with a distinct mid-day low point. Relative to other migrating shorebirds, Buff-breasted Sandpipers spent a significant proportion of their time in social interactions including courtship displays. Our results show that the primary use of upland agricultural fields by migrating Buff-breasted Sandpipers is foraging while wetlands are used for maintenance and resting. The importance of foraging in row crop fields suggests that both the quality of food resources available in fields and the possible risks from dietary exposure to agricultural chemicals will be important to consider when developing conservation plans for Buff-breasted Sandpipers migrating through the Great Plains.
Knowledge of historical changes in species range distribution provides context for investigating adaptive potential and dispersal ability. This is valuable for predicting the potential impact of environmental change on species of interest. Butterflies are one of the most important taxa for studying such impacts, and Heteronympha merope has the potential to provide a particularly valuable model, in part due to the existence of historical data on morphological traits and glycolytic enzyme variation. This study investigates the population genetic structure and phylogeography of H. merope, comparing the relative resolution achieved through partial DNA sequences of two mitochondrial loci, COI and ND5. These data are used to define the relationship between subspecies, showing that the subspecies are reciprocally monophyletic. On this basis, the Western Australian subspecies H. m. duboulayi is genetically distinct from the two eastern subspecies. Throughout the eastern part of the range, levels of migration and the timing of key population splits of potential relevance to climatic adaptation are estimated and indicate Late Pleistocene divergence both of the Tasmanian subspecies and of an isolated northern population from the eastern mainland subspecies H. m. merope. This information is then used to revisit historical data and provides support for the importance of clinal variation in wing characters, as well as evidence for selective pressure acting on allozyme loci phosphoglucose isomerase and phosphoglucomutase in H. merope. The study has thus confirmed the value of H. merope as a model organism for measuring responses to environmental change, offering the opportunity to focus on isolated populations, as well as a latitudinal gradient, and to use historical changes to test the accuracy of predictions for the future.
Chronic wasting disease (CWD) of cervids is a prion disease distinguished by high levels of transmissibility, wherein bodily fluids and excretions are thought to play an important role. Using cervid bioassay and established CWD detection methods, we have previously identified infectious prions in saliva and blood but not urine or feces of CWD+ donors. More recently, we identified very low concentrations of CWD prions in urine of deer by cervid PrP transgenic (Tg[CerPrP]) mouse bioassay and serial protein misfolding cyclic amplification (sPMCA). This finding led us to examine further our initial cervid bioassay experiments using sPMCA. We sought to investigate whether conventional test-negative deer, previously exposed orally to urine and feces from CWD+ sources, may be harboring low level CWD infection not evident in the 19 month observation period. We further attempted to determine the peripheral PrPCWD distribution in these animals. Various neural and lymphoid tissues from conventional test-negative deer were reanalyzed for CWD prions by sPMCA and cervid transgenic mouse bioassay in parallel with appropriate tissue-matched positive and negative controls. PrPCWD was detected in the tissues of orally exposed deer by both sPMCA and Tg[CerPrP] mouse bioassay; each assay revealed very low levels of CWD prions previously undetectable by western blot, ELISA, or IHC. Serial PMCA analysis of individual tissues identified that obex alone was positive in 4 of 5 urine/feces exposed deer. PrPCWD was amplified from both lymphoid and neural tissues of positive control deer but not from identical tissues of negative control deer. Detection of subclinical infection in deer orally exposed to urine and feces (1) suggests that a prolonged subclinical state can exist, necessitating observation periods in excess of two years to detect CWD infection, and (2) illustrates the sensitive and specific application of sPMCA in the diagnosis of low-level prion infection. Based on these results, it is possible that low doses of prions, e.g. following oral exposure to urine and saliva of CWD-infected deer, bypass significant amplification in the LRS, perhaps utilizing a neural conduit between the alimentary tract and CNS, as has been demonstrated in some other prion diseases.
The vomeronasal system (VNS) mediates pheromonal communication in mammals. From the vomeronasal organ, two populations of sensory neurons, expressing either Gαi2 or Gαo proteins, send projections that end in glomeruli distributed either at the rostral or caudal half of the accessory olfactory bulb (AOB), respectively. Neurons at the AOB contact glomeruli of a single subpopulation. The dichotomic segregation of AOB glomeruli has been described in opossums, rodents and rabbits, while Primates and Laurasiatheres present the Gαi2-pathway only, or none at all (such as apes, some bats and aquatic species). We studied the AOB of the Madagascan lesser tenrec Echinops telfairi (Afrotheria: Afrosoricida) and found that Gαi2 and Gαo proteins are expressed in rostral and caudal glomeruli, respectively. However, the segregation of vomeronasal glomeruli at the AOB is not exclusive, as both pathways contained some glomeruli transposed into the adjoining subdomain. Moreover, some glomeruli seem to contain intermingled afferences from both pathways. Both the transposition and heterogeneity of vomeronasal afferences are features, to our knowledge, never reported before. The organization of AOB glomeruli suggests that synaptic integration might occur at the glomerular layer. Whether intrinsic AOB neurons may make synaptic contact with axon terminals of both subpopulations is an interesting possibility that would expand our understanding about the integration of vomeronasal pathways.
Sarcopenia is a major public health problem in industrialized nations, placing an increasing burden on public healthcare systems because the loss of skeletal muscle mass and strength that characterizes this affection increases the dependence and the risk of injury caused by sudden falls in elderly people. Albeit exercise and caloric restriction improve sarcopenia-associated decline of the muscular performances, a more suitable and focused pharmacological treatment is still lacking. In order to evaluate such a possible treatment, we investigated the effects of EGb 761, a Ginkgo biloba extract used in chronic age-dependent neurological disorders, on the function of the soleus muscle in aged rats. EGb 761 induced a gain in muscular mass that was associated with an improvement of the muscular performances as assessed by biochemical and electrophysiological tests. DNA microarray analysis shows that these modifications are accompanied by the transcriptional reprogramming of genes related to myogenesis through the TGFβ signaling pathway and to energy production via fatty acids and glucose oxidation. EGb 761 restored a more juvenile gene expression pattern by regenerating the aged muscle and reversing the age-related metabolic shift from lipids to glucose utilization. Thus, EGb 761 may represent a novel treatment for sarcopenia both more manageable and less cumbersome than exercise and caloric restriction.
As you know you can see everyone who's registered for the conference, but I highlight 4-6 participants every day as this may be an easier way for you to digest the list. You can also look at the Program so see who is doing what.
Mauricio Borgen is the IT Administrator at Athenix Corp, a agricultural and chemical biotechnology company, and a veteran of all our conferences over the years.
There are 22 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week - you go and look for your own favourites:
Comparing patterns of divergence among separate lineages or groups has posed an especially difficult challenge for biologists. Recently a new, conceptually simple methodology called the "ordered-axis plot" approach was introduced for the purpose of comparing patterns of diversity in a common morphospace. This technique involves a combination of principal components analysis (PCA) and linear regression. Given the common use of these statistics the potential for the widespread use of the ordered axis approach is high. However, there are a number of drawbacks to this approach, most notably that lineages with the greatest amount of variance will largely bias interpretations from analyses involving a common morphospace. Therefore, without meeting a set of a priori requirements regarding data structure the ordered-axis plot approach will likely produce misleading results. Morphological data sets from cichlid fishes endemic to Lakes Tanganyika, Malawi, and Victoria were used to statistically demonstrate how separate groups can have differing contributions to a common morphospace produced by a PCA. Through a matrix superimposition of eigenvectors (scale-free trajectories of variation identified by PCA) we show that some groups contribute more to the trajectories of variation identified in a common morphospace. Furthermore, through a set of randomization tests we show that a common morphospace model partitions variation differently than group-specific models. Finally, we demonstrate how these limitations may influence an ordered-axis plot approach by performing a comparison on data sets with known alterations in covariance structure. Using these results we provide a set of criteria that must be met before a common morphospace can be reliably used. Our results suggest that a common morphospace produced by PCA would not be useful for producing biologically meaningful results unless a restrictive set of criteria are met. We therefore suggest biologists be aware of the limitations of the ordered-axis plot approach before employing it on their own data, and possibly consider other, less restrictive methods for addressing the same question.
Although copy number variation (CNV) has recently received much attention as a form of structure variation within the human genome, knowledge is still inadequate on fundamental CNV characteristics such as occurrence rate, genomic distribution and ethnic differentiation. In the present study, we used the Affymetrix GeneChip® Mapping 500K Array to discover and characterize CNVs in the human genome and to study ethnic differences of CNVs between Caucasians and Asians. Three thousand and nineteen CNVs, including 2381 CNVs in autosomes and 638 CNVs in X chromosome, from 985 Caucasian and 692 Asian individuals were identified, with a mean length of 296 kb. Among these CNVs, 190 had frequencies greater than 1% in at least one ethnic group, and 109 showed significant ethnic differences in frequencies (p<0.01). After merging overlapping CNVs, 1135 copy number variation regions (CNVRs), covering approximately 439 Mb (14.3%) of the human genome, were obtained. Our findings of ethnic differentiation of CNVs, along with the newly constructed CNV genomic map, extend our knowledge on the structural variation in the human genome and may furnish a basis for understanding the genomic differentiation of complex traits across ethnic groups.
In September 2007, an outbreak of acute hemorrhagic conjunctivitis (AHC) occurred in Keelung City and spread to Taipei City. In response to the epidemic, a new crisis management program was implemented and tested in Taipei. Having noticed that transmission surged on weekends during the Keelung epidemic, Taipei City launched a multi-channel mass risk communications program that included short message service (SMS) messages sent directly to approximately 2.2 million Taipei residents on Friday, October 12th, 2007. The public was told to keep symptomatic students from schools and was provided guidelines for preventing the spread of the disease at home. Epidemiological characteristics of Taipei's outbreak were analyzed from 461 sampled AHC cases. Median time from exposure to onset of the disease was 1 day. This was significantly shorter for cases occurring in family clusters than in class clusters (mean±SD: 2.6±3.2 vs. 4.39±4.82 days, p = 0.03), as well as for cases occurring in larger family clusters as opposed to smaller ones (1.2±1.7 days vs. 3.9±4.0 days, p<0.01). Taipei's program had a significant impact on patient compliance. Home confinement of symptomatic children increased from 10% to 60% (p<0.05) and helped curb the spread of AHC. Taipei experienced a rapid decrease in AHC cases between the Friday of the SMS announcement and the following Monday, October 15, (0.70% vs. 0.36%). By October 26, AHC cases reduced to 0.01%. The success of this risk communication program in Taipei (as compared to Keelung) is further reflected through rapid improvements in three epidemic indicators: (1) significantly lower crude attack rates (1.95% vs. 14.92%, p<0.001), (2) a short epidemic period of AHC (13 vs. 34 days), and (3) a quick drop in risk level (1~2 weeks) in Taipei districts that border Keelung (the original domestic epicenter). The timely launch of this systematic, communication-based intervention proved effective at preventing a dangerous spike in AHC and was able to bring this high-risk disease under control. We recommend that public health officials incorporate similar methods into existing guidelines for preventing pandemic influenza and other emerging infectious diseases.
Epidemiological studies suggest that allogeneic immunity may inhibit HIV-1 transmission from mother to baby and is less frequent in multiparous than uniparous women. Alloimmune responses may also be elicited during unprotected heterosexual intercourse, which is associated ex vivo with resistance to HIV infection. The investigation was carried out in well-defined heterosexual and homosexual monogamous partners, practising unprotected sex and a heterosexual cohort practising protected sex. Allogeneic CD4+ and CD8+ T cell proliferative responses were elicited by stimulating PBMC with the partners' irradiated monocytes and compared with 3rd party unrelated monocytes, using the CFSE method. Significant increase in allogeneic proliferative responses was found in the CD4+ and CD8+ T cells to the partners' irradiated monocytes, as compared with 3rd party unrelated monocytes (p≤0.001). However, a significant decrease in proliferative responses, especially of CD8+ T cells to the partners' compared with 3rd party monocytes was consistent with tolerization, in both the heterosexual and homosexual partners (p<0.01). Examination of CD4+CD25+FoxP3+ regulatory T cells by flow cytometry revealed a significantly greater proportion of these cells in the homosexual than heterosexual partners practising unprotected sex (p<0.05). Ex vivo studies of infectivity of PBMC with HIV-1 showed significantly greater inhibition of infectivity of PBMC from heterosexual subjects practising unprotected compared with those practising protected sex (p = 0.02). Both heterosexual and homosexual monogamous partners practising unprotected sex develop allogeneic CD4+ and CD8+ T cell proliferative responses to the partners' unmatched cells and a minority may be tolerized. However, a greater proportion of homosexual rather than heterosexual partners developed CD4+CD25FoxP3+ regulatory T cells. These results, in addition to finding greater inhibition of HIV-1 infectivity in PBMC ex vivo in heterosexual partners practising unprotected, compared with those practising protected sex, suggest that allogeneic immunity may play a significant role in the immuno-pathogenesis of HIV-1 infection.
In today's podcast Ilona interviews Felice Frankel, a Senior Research Fellow at Harvard and a Research Scientist at MIT. Felice is a photographer who is keenly interested in visual communication of complex concepts. To that end, she has written three books about the subject. Felice's recent effort to bring visual representation of science concepts into education culminated in the NSF-funded Picturing to Learn project. Her most recent book, No Small Matter, written with George Whitesides, illustrates nanoscience with metaphor. Listen to this podcast to hear about how creating visual representations of science can change the way science is taught. A full transcript of the podcast is below. [19:23]
Felice will be at ScienceOnline2010, leading a session on Art and Science: Visual Metaphors. Her book, No Small Matter, arrived the other day and Bride Of Coturnix and I were oohing and aahing over it - it is beautiful and brilliant.
The second annual National Day of Listening - celebrated on Friday, November 27, 2009 - is just around the corner! With your help, we hope to make the National Day of Listening an ongoing holiday tradition, when all Americans set aside time on the day after Thanksgiving to honor a friend, loved one, or member of their community by interviewing them about their lives and preserving that interview for generations to come.
We'd like to ask you to take part in this year's National Day of Listening by conducting an interview with someone you know and blogging about the experience. Here are some tips:
1. Let your fingers do the talking! Include details about why the National Day of Listening is meaningful for you and how you plan to participate.
2. StoryCorps' Do-It-Yourself Instruction Guide has all the information you need to get started.
3. Pledge to participate! Tell us how you plan to get involved, and read about all the other ways people throughout the country are participating.
4. Post StoryCorps' web banners, logos, customizable web text and Facebook fan button on your blog. Download these materials at our Share page.
Reminder: Deadline is December 1st at midnight EST!
Here are the submissions for OpenLab 2009 to date (under the fold). You can buy the 2006, 2007 and 2008 editions at Lulu.com. Please use the submission form to add more of your and other people's posts (remember that we are looking for original poems, art, cartoons and comics, as well as essays):
Make sure that the submitted posts are possible (and relatively easy) to convert into print. Posts that rely too much on video, audio, color photographs, copyrighted images, or multitudes of links just won't do (I won't even include them here - there are about 520 posts here so the judges have a lot of good posts to read already so no need to bother them with obviously inappropriate entries).
Continuing with the introductions to the sessions on the Program, here is what will happen on Saturday, January 16th at 11:30am - 12:35pm:
A.Legal Aspects of publishing, sharing and blogging science - Victoria Stodden
Description: Not giving legal advice, but discussion of CC-licences, copyright, Fair Use, libel laws, etc. Discuss here.
B.Shakespeare wasn't a semantic web guy - Jonathan Rees
Description: That which we call a rose, by any other name, wouldn't be identified by a computer as a rose. This talk will go through the Shared Name initiative which promotes community-wide use of shared names for records from public databases. The goal is to have a significant effect on the practice of bioinformatics by making it easier to share and link data sets and tools across projects. Selecting and maintaining names is a serious capacity building problem for moving the RDF world from the hacker and hobbyist community to the regular user. And a growing body of experience emphasizes that for any solution to be generally adopted, it must not only be technically sound, but also serve and empower the community of users. Discuss here.
Description: Not so long ago, "citizen scientist" would have seemed to be a contradiction in terms. Science is traditionally something done by people in lab coats who hold PhDs. As with classical music or acting, amateurs might be able to appreciate science, but they could not contribute to it. Today, however, enabled by technology and empowered by social change, science-interested laypeople are transforming the way science gets done. Through a myriad of different projects, citizen scientists are collaborating with professionals, conducting field studies, and adding valuable local detail to research. Discuss here.
Description: Debris in the North Pacific Gyre received unprecedented attention in 2009 with voyages from the Algalita Marine Research Foundation, Project Kaisei, and the Scripps Institution of Oceanography. Each voyage integrated online outreach into its mission, but emphasized very different aspects of the problem. What are the challenges of creating a major outreach effort from one of the most isolated places on earth? How can scientists, journalists, and educators balance "exciting findings live from the field!" with "highly preliminary unpublished non-peer-reviewed data that our labwork might contradict"? And why is the public so interested in the issue of trash in the ocean, anyway? Discuss here.
Description: A picture is not only worth a thousand words---it is also worth a thousand numbers. This session will focus on ways to move from raw quantitative and qualitative data to a variety of visuals that communicate with all audiences. Discuss here.
I don't possess a lot of self-confidence. I'm an actor so I simply act confident every time I hit the stage. I am consumed with the fear of failing. Reaching deep down and finding confidence has made all my dreams come true.
As you know you can see everyone who's registered for the conference, but I highlight 4-6 participants every day as this may be an easier way for you to digest the list. You can also look at the Program so see who is doing what.
Hope Leman is a Research Information Technologist at Samaritan Health Services. She runs ScanGrants (a free, subscribable (via email or RSS) online listing of grant opportunities, prizes and scholarships in the health and life sciences and community service fields), tweets and blogs on Significant Science. At the conference, Hope will do a demo of ScanGrants.
Ernie Hood is a freelance science writer and he hosts a weekly science radio show - Radio In Vivo - at the local radio station WCOM-FM in Carrboro, NC. Ernie is currently presiding over SCONC - the organization of Science Communicators of North Carolina.
Elle Cayabyab Gitlin writes for Ars Technica, blogs and tweets. And she is always a great help to us at the conference, every year volunteering to help.
The North Carolina Museum of Natural Sciences hosts the final offering of its Charles Darwin Lecture Series on Tuesday, November 24 -- the 150th anniversary of Darwin's landmark publication of "The Origin of Species." Join Museum paleontologist and science historian Paul Brinkman for a free presentation titled "Charles Darwin's Beagle Voyage and the Origin of 'The Origin.'"
Dr. Brinkman completed his PhD in History of Science at the University of Minnesota with research in the history of 19th-century natural sciences, especially geology and paleontology. He has published a number of articles on Darwin, museum history, and the history of American vertebrate paleontology. His second book, The Second American Jurassic Dinosaur Rush, is due out next year from the University of Chicago Press.
Please RSVP to museum.reservations@ncmail.net -- be sure to specify the event name and date. This lecture is free of charge and seating is on a first-come, first-served basis. Doors to the Museum and auditorium will open at 6:00 pm and the presentation will begin at 6:30 pm.
The Museum, in collaboration with the National Evolutionary Synthesis Center (NESCent) and the W.M. Keck Center for Behavioral Biology at North Carolina State University, has presented several talks throughout 2009 to commemorate the bicentennial of Charles Darwin's birth and the 150th anniversary of the publication of "The Origin of Species." The series showcases the Triangle region of North Carolina as a hot spot for evolutionary biology research and features prominent researchers from area universities. Stay tuned to the Museum's website [www.naturalsciences.org] for Darwin-themed events scheduled for 2010.
Friday - PLoS Genetics, Pathogens, Computational Biology and ONE published today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week - you go and look for your own favourites:
Circadian clocks are endogenous timing mechanisms that allow living organisms to coordinate their activities with daily environmental fluctuations. In cyanobacteria, almost all the genes are rhythmically expressed with the same ~24 h period yet exhibit a variety of phase relationships and waveforms. Remarkably, the core pacemaker ticks robustly via simple biochemical reactions carried out by three Kai proteins: KaiC undergoes circadian phosphorylation in the presence of KaiA, KaiB and ATP. In this work, we propose a reaction network modeling the Kai oscillator based on the differentiation of dual phosphorylation sites. We found a dynamic diversity in KaiC phosphorylation which may serve as a potential regulatory mechanism related to the diverse-phased genome-wide expressions in cyanobacteria. In addition, we deduce that each KaiC hexamer is a single oscillator in regulating its own phosphorylation and interactions with KaiA or/and KaiB. In complex organisms, a number of key clock components possess similar activities (e.g., phosphorylation) with multiple nonequivalent active sites, and they may also show some unusual dynamic features that are embedded in the proteins' own reaction networks. We hope our work could be helpful to study the correlations between gene expressions and circadian rhythm in prokaryotic cells, even in eukaryotic cells.
For many animals, including rats, accurate spatial memory over relatively large areas is important in order to find food and shelter. Just as unique points in time can be efficiently represented by combinations of repeating elements like hours, days, and months, points in space can be represented as combinations of elements that repeat at different spatial scales. Just such a code has been identified in the brains of rats and it shows an intriguing triangular spacing of encoded locations. Two different explanations have been developed as to what general mechanism in the brain might be able to generate this unusual code. However, to date there is not conclusive experimental evidence indicating whether either of the two explanations is correct. Here we show in detail that one of the explanations, called oscillatory interference, has specific requirements regarding the amount of variability in the system that implements it. We then report data experimentally examining candidate systems to evaluate their levels of noise. The large amount of noise that we find presents a challenge to the currently suggested biological implementations of oscillatory interference, but it does not provide support for the alternative explanation.
Why should you read about the maize genome? Now that so many eukaryotic genomes are available, it's easy to be blasé... just another few billion bases, grist for constructing gene trees. Why is this new information, so recently shared, worth considering? I am convinced, as I propose you will be too as you read on, that both geneticists and genome consumers will benefit from the first description of the B73 maize genome [1] and equally so from the companion papers compiled in this special collection (http://collections.plos.org/plosgenetics/maize.php ).
The relative contributions of natural selection and random genetic drift are a major source of debate in the study of gene expression evolution, which is hypothesized to serve as a bridge from molecular to phenotypic evolution. It has been suggested that the conflict between views is caused by the lack of a definite model of the neutral hypothesis, which can describe the long-run behavior of evolutionary change in mRNA abundance. Therefore previous studies have used inadequate analogies with the neutral prediction of other phenomena, such as amino acid or nucleotide sequence evolution, as the null hypothesis of their statistical inference. In this study, we introduced two novel theoretical models, one based on neutral drift and the other assuming natural selection, by focusing on a common property of the distribution of mRNA abundance among a variety of eukaryotic cells, which reflects the result of long-term evolution. Our results demonstrated that (1) our models can reproduce two independently found phenomena simultaneously: the time development of gene expression divergence and Zipf's law of the transcriptome; (2) cytological constraints can be explicitly formulated to describe long-term evolution; (3) the model assuming that natural selection optimized relative mRNA abundance was more consistent with previously published observations than the model of optimized absolute mRNA abundances. The models introduced in this study give a formulation of evolutionary change in the mRNA abundance of each gene as a stochastic process, on the basis of previously published observations. This model provides a foundation for interpreting observed data in studies of gene expression evolution, including identifying an adequate time scale for discriminating the effect of natural selection from that of random genetic drift of selectively neutral variations.
Smell provides important information about the quality of food and drink. Most well-known for their expertise in wine tasting, sommeliers sniff out the aroma of wine and describe them using beautiful metaphors. In contrast, electronic noses, devices that mimic our olfactory recognition system, also detect smells using their sensors but describe them using electronic signals. These devices have been used to judge the freshness of food or detect the presence of pathogenic microorganisms. However, unlike information from gas chromatography, it is difficult to compare odour information collected by these devices because they are made for smelling specific smells and their data are relative intensities. Here, we demonstrate the use of an absolute-value description method using known smell metaphors, and early detection of yeast using the method. This technique may help distinguishing microbial-contamination of food products earlier, or improvement of the food-product qualities.
Recent literature documented the presence of spatial-temporal interactions in the human brain. The aim of the present study was to verify whether representation of past and future is also mapped onto spatial representations and whether the cerebellum may be a neural substrate for linking space and time in the linguistic domain. We asked whether processing of the tense of a verb is influenced by the space where response takes place and by the semantics of the verb. Responses to past tense were facilitated in the left space while responses to future tense were facilitated in the right space. Repetitive transcranial magnetic stimulation (rTMS) of the right cerebellum selectively slowed down responses to future tense of action verbs; rTMS of both cerebellar hemispheres decreased accuracy of responses to past tense in the left space and to future tense in the right space for non-verbs, and to future tense in the right space for state verbs. The results suggest that representation of past and future is mapped onto spatial formats and that motor action could represent the link between spatial and temporal dimensions. Right cerebellar, left motor brain networks could be part of the prospective brain, whose primary function is to use past experiences to anticipate future events. Both cerebellar hemispheres could play a role in establishing the grammatical rules for verb conjugation.
Genetic differences both between individuals and populations are studied for their evolutionary relevance and for their potential medical applications. Most of the genetic differentiation among populations are caused by random drift that should affect all loci across the genome in a similar manner. When a locus shows extraordinary high or low levels of population differentiation, this may be interpreted as evidence for natural selection. The most used measure of population differentiation was devised by Wright and is known as fixation index, or FST. We performed a genome-wide estimation of FST on about 4 millions of SNPs from HapMap project data. We demonstrated a heterogeneous distribution of FST values between autosomes and heterochromosomes. When we compared the FST values obtained in this study with another evolutionary measure obtained by comparative interspecific approach, we found that genes under positive selection appeared to show low levels of population differentiation. We applied a gene set approach, widely used for microarray data analysis, to detect functional pathways under selection. We found that one pathway related to antigen processing and presentation showed low levels of FST, while several pathways related to cell signalling, growth and morphogenesis showed high FST values. Finally, we detected a signature of selection within genes associated with human complex diseases. These results can help to identify which process occurred during human evolution and adaptation to different environments. They also support the hypothesis that common diseases could have a genetic background shaped by human evolution.
Niche theory is central to understanding how species respond geographically to climate change. It defines a species' realized niche in a biological community, its fundamental niche as determined by physiology, and its potential niche--the fundamental niche in a given environment or geographic space. However, most predictions of the effects of climate change on species' distributions are limited to correlative models of the realized niche, which assume that species are in distributional equilibrium with respect to the variables or gradients included in the model. Here, I present a mechanistic niche model that measures species' responses to major seasonal temperature gradients that interact with the physiology of the organism. I then use lethal physiological temperatures to parameterize the model for bird species in North and South America and show that most focal bird species are not in direct physiological equilibrium with the gradients. Results also show that most focal bird species possess broad thermal tolerances encompassing novel climates that could become available with climate change. I conclude with discussion of how mechanistic niche models may be used to (i) gain insights into the processes that cause species to respond to climate change and (ii) build more accurate correlative distribution models in birds and other species.
Continuing with the series (I get more and more feedback that people love this) introducing, a few at a time, the participants of the ScienceOnline2010 conference. You can also look at the Program so see who is doing what.
Anil Dash is a pioneer blogger (and of course twitterer) and one of the founders of Six Apart, the company that built blogging platforms including MoveableType (which is used by Scienceblogs.com) and Typepad.
Just yesterday, he made an official announcement that he will be leading Expert Labs (also on Twitter) which is a new project (largely run/funded by AAAS) to facilitate feedback by the experts (including scientists, of course) to the Obama Administration and other government officials. Read the press release, the early media coverage (this one is much better) , an interview with Anil (pdf) and a video. Interestingly, Anil got this job due to writing a blog post stating that the executive branch of the federal government of the United States was the "Most Interesting New Tech Startup of 2009".
At ScienceOnline2010, Anil will run the session Government 2.0 the main purpose of which is for him to get feedback from the leaders of the science and Web community on how to make Expert Labs work the best it possibly can.
A short summary article by Lindsey was then published in the New York Times (which, while making no promises, was interested in the story from the start). That article (and especially in comparison to her blogging) was greeted by quite a lot of commentary, some by media watchers and journalists, some by scientists. See the reactions, for example, by Megan Garber, Miriam Goldstein, John Zhu, Martin Robbins, Mathew Ingram and Sheril Kirshenbaum (and Sheril again - read the comment thread).
The voyage, and the reporting from it (both on traditional and modern media platforms), brought into light the differences between the goals, needs, methods and ethics of journalists and those of scientists. What those differences are, and how they can be surmounted so scientists and journalists can work together and each do a better job, will be the topic of the session that Lindsay will be co-moderating - Talking Trash - which promises to be quite exciting!
Ben MacNeill is a designer here in Chapel Hill. I first met Ben at the 2005 BloggerCon at UNC. When his daughter Trixie was born he started a blog, Trixie Update, on which he recorded and graphed everything he could think of about his daughter's daily patterns: when she slept, ate, had a diaper change, etc. I commented on this, from a perspective of a chronobiologist, in an old blog post about the development and consolidation of circadian rhythms and sleep patterns in human infants. Trixie is far too old to have diapers changed any more, but the setup continues. Ben has developed the software further and is now offering it as an iPhone (or Web) application - the Trixie Tracker which you can use, if you are a new parent, to track everything you want about your baby (and perhaps detect early if something suddenly changes and perhaps requires medical attention). Ben is also on Twitter.
Elia Ben-Ari is a freelance science writer and editor who has published in many good venues over the years. She is active on Twitter. Her latest article (which, understandably, garnered quite a lot of interest online) is Twitter: What's All the Chirping About?
Wayne Sutton is a social media maven. He is a partner of social media marketing agency OurHashtag, the co-host of a social media podcast at TalkSocialNews.com, the host of the online video show WayneSutton.TV, and a veteran blogger. He is on every social networking site imaginable, but here let's just link to his Twitter account. At ScienceOnline2010, Wayne will do an Ignite talk "Why Triangle is Better than Silicon Valley".
There are 25 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week - you go and look for your own favourites:
Despite its appearing to be a simple question to answer, there has been no consensus as to whether or not the alignments of ancient Greek temples reflect astronomical intentions. Here I present the results of a survey of archaic and classical Greek temples in Sicily and compare them with temples in Greece. Using a binomial test I show strong evidence that there is a preference for solar orientations. I then speculate that differences in alignment patterns between Sicily and Greece reflect differing pressures in the expression of ethnic identity.
Medical technologies are indispensable to modern medicine. However, they have become exceedingly expensive and complex and are not available to the economically disadvantaged majority of the world population in underdeveloped as well as developed parts of the world. For example, according to the World Health Organization about two thirds of the world population does not have access to medical imaging. In this paper we introduce a new medical technology paradigm centered on wireless technology and cloud computing that was designed to overcome the problems of increasing health technology costs. We demonstrate the value of the concept with an example; the design of a wireless, distributed network and central (cloud) computing enabled three-dimensional (3-D) ultrasound system. Specifically, we demonstrate the feasibility of producing a 3-D high end ultrasound scan at a central computing facility using the raw data acquired at the remote patient site with an inexpensive low end ultrasound transducer designed for 2-D, through a mobile device and wireless connection link between them. Producing high-end 3D ultrasound images with simple low-end transducers reduces the cost of imaging by orders of magnitude. It also removes the requirement of having a highly trained imaging expert at the patient site, since the need for hand-eye coordination and the ability to reconstruct a 3-D mental image from 2-D scans, which is a necessity for high quality ultrasound imaging, is eliminated. This could enable relatively untrained medical workers in developing nations to administer imaging and a more accurate diagnosis, effectively saving the lives of people.
Fragile X syndrome (FXS) is one of the most common known causes of inherited mental retardation. The gene mutated in FXS is named FMR1, and is well conserved from human to Drosophila. In order to generate a genetic tool to study FMR1 function during vertebrate development, we generated two mutant alleles of the fmr1 gene in zebrafish. Both alleles produce no detectable Fmr protein, and produce viable and fertile progeny with lack of obvious phenotypic features. This is in sharp contrast to published results based on morpholino mediated knock-down of fmr1, reporting defects in craniofacial development and neuronal branching in embryos. These phenotypes we specifically addressed in our knock-out animals, revealing no significant deviations from wild-type animals, suggesting that the published morpholino based fmr1 phenotypes are potential experimental artifacts. Therefore, their relation to fmr1 biology is questionable and morpholino induced fmr1 phenotypes should be avoided in screens for potential drugs suitable for the treatment of FXS. Importantly, a true genetic zebrafish model is now available which can be used to study FXS and to derive potential drugs for FXS treatment.
It is well known that facial expressions represent important social cues. In humans expressing facial emotion, fear may be configured to maximize sensory exposure (e.g., increases visual input) whereas disgust can reduce sensory exposure (e.g., decreases visual input). To investigate whether such effects also extend to the attentional system, we used the "attentional blink" (AB) paradigm. Many studies have documented that the second target (T2) of a pair is typically missed when presented within a time window of about 200-500 ms from the first to-be-detected target (T1; i.e., the AB effect). It has recently been proposed that the AB effect depends on the efficiency of a gating system which facilitates the entrance of relevant input into working memory, while inhibiting irrelevant input. Following the inhibitory response on post T1 distractors, prolonged inhibition of the subsequent T2 is observed. In the present study, we hypothesized that processing facial expressions of emotion would influence this attentional gating. Fearful faces would increase but disgust faces would decrease inhibition of the second target. We showed that processing fearful versus disgust faces has different effects on these attentional processes. We found that processing fear faces impaired the detection of T2 to a greater extent than did the processing disgust faces. This finding implies emotion-specific modulation of attention. Based on the recent literature on attention, our finding suggests that processing fear-related stimuli exerts greater inhibitory responses on distractors relative to processing disgust-related stimuli. This finding is of particular interest for researchers examining the influence of emotional processing on attention and memory in both clinical and normal populations. For example, future research could extend upon the current study to examine whether inhibitory processes invoked by fear-related stimuli may be the mechanism underlying the enhanced learning of fear-related stimuli.
Chemicals are used on bed nets in order to prevent infected bites and to kill aggressive malaria vectors. Because pyrethroid resistance has become widespread in the main malaria vectors, research for alternative active ingredients becomes urgent. Mixing a repellent and a non-pyrethroid insecticide seemed to be a promising tool as mixtures in the laboratory showed the same features as pyrethroids. We present here the results of two trials run against free-flying Anopheles gambiae populations comparing the effects of two insect repellents (either DEET or KBR 3023, also known as icaridin) and an organophosphate insecticide at low-doses (pirimiphos-methyl, PM) used alone and in combination on bed nets. We showed that mixtures of PM and the repellents induced higher exophily, blood feeding inhibition and mortality among wild susceptible and resistant malaria vectors than compounds used alone. Nevertheless the synergistic interactions are only involved in the high mortality induced by the two mixtures. These field trials argue in favour of the strategy of mixing repellent and organophosphate on bed nets to better control resistant malaria vectors.
Despite remarkable progress in treatment of chronic heart failure (CHF) over the last two decades, mortality, personal suffering and cost remain staggering, and effective interventions are still a challenge. Previously we reported that a blueberry-enriched diet (BD) attenuated necroapoptosis and inflammation in periinfarct area in a rat model of myocardial infarction (MI). To test the hypothesis that BD will attenuate the course of CHF, including mortality and cardiac remodeling during the first year after induction of MI in rats. Two weeks after coronary artery ligation, rats were divided into two groups of similar average MI size, measured by echocardiography, and then12-mo dietary regimens were initiated as follows: ad libitum regular diet (control, CD, n = 27) and isocaloric food with 2% blueberry supplement (BD, n = 27) also available ad libitum. These dietary groups were compared to each other and to sham group (SH). Mortality over the 12 mo was reduced by 22% in BD compared with CD (p<0.01). In the course of developing CHF, BD had no effect on the body weight, heart rate or blood pressure. Bi-monthly Echo revealed significant attenuation of the LV chamber remodeling, LV posterior wall thinning, and MI expansion in BD compared with CD. In fact, BD arrested the MI expansion. This is the first experimental evidence that a blueberry-enriched diet has positive effects on the course of CHF and thus warrants consideration for clinical evaluation.
Where: National Evolutionary Synthesis Center in Durham
Please join us to commemorate Charles Darwin's 200th birthday and the 150th anniversary of "The Origin of Species."
Learn about the wild world of Ice Age carnivores, brainy birds, and other creatures Darwin missed. Our tour guides will be four postdocs on the frontiers of biology.
We'll begin at 6pm at the National Evolutionary Synthesis Center in Durham. Parking is free.
National Evolutionary Synthesis Center (NESCent)
2024 W. Main Street, Suite A200
Durham, NC 27705
Map: http://bit.ly/rGmKM
Travel Directions: The National Evolutionary Synthesis Center is near the corner of 9th St. and W. Main St. in Durham, on the 2nd floor of the Erwin Mill Building. Free parking is available in front of the building.
