Post List

  • September 23, 2011
  • 05:16 AM

An impossible star?

by Kelly Oakes in Basic Space

In the beginning, the only elements that existed were hydrogen, helium and very small amounts of lithium...... Read more »

Caffau E, Bonifacio P, François P, Sbordone L, Monaco L, Spite M, Spite F, Ludwig HG, Cayrel R, Zaggia S.... (2011) An extremely primitive star in the Galactic halo. Nature, 477(7362), 67-9. PMID: 21886158  

  • September 23, 2011
  • 04:28 AM

A case report of localised fibrofolliculomas

by Joana Guedes in BHD Research Blog

In order to further understand the clinical aspects and symptoms of BHD syndrome, it is important that novel findings discovered during patient analysis are published in case reports. This assists in unravelling genotype-phenotype correlations, and also in identifying trends, for … Continue reading →... Read more »

Alonso-González J, Rodríguez-Pazos L, Fernández-Redondo V, Vega-Gliemmo A, & Toribio J. (2011) Birt-Hogg-Dubé syndrome in a patient with localized fibrofolliculomas and a novel mutation in the FLCN gene. International journal of dermatology, 50(8), 968-71. PMID: 21781069  

Kluger N, Giraud S, Coupier I, Avril MF, Dereure O, Guillot B, Richard S, & Bessis D. (2010) Birt-Hogg-Dubé syndrome: clinical and genetic studies of 10 French families. The British journal of dermatology, 162(3), 527-37. PMID: 19785621  

Schulz T, Ebschner U, & Hartschuh W. (2001) Localized Birt-Hogg-Dubé syndrome with prominent perivascular fibromas. The American Journal of dermatopathology, 23(2), 149-53. PMID: 11285413  

Starink TM, Houweling AC, van Doorn MB, Leter EM, Jaspars EH, van Moorselaar RJ, Postmus PE, Johannesma PC, van Waesberghe JH, Ploeger MH.... (2011) Familial multiple discoid fibromas: A look-alike of Birt-Hogg-Dubé syndrome not linked to the FLCN locus. Journal of the American Academy of Dermatology. PMID: 21794948  

  • September 23, 2011
  • 03:43 AM

Afraid of the dark

by Megan in Rigel

I've never been afraid of the dark.; When it's all you've ever known, it seems a rather silly notion.; But now... well, this seems different somehow.; Now we're all frightened.It wasn't always like this.; We all grew up with the stories about the old times, when there were colonies every few parsecs, all set on planets (artificial or otherwise) around healthy stars, and supply stations strung along the major trade routes likes beads of water on an invisible web.; The galaxy thrived back then, or so the stories go.; Civilisation reaching ever outwards, colonising, trading, cooperating, and fighting, naturally.; There was rarely ever total peace, not in our nature say the historians.; But it's all long gone now.Slowly, imperceptibly at first, night began to fall across the universe.; Complete and total darkness, the end of all things.; Our own star (we knew it as Suryan) faded from glory long before I was born.; I've never known real daylight, never felt the warmth of the midday sunlight on my skin.; Growing up, we were all told the stories and legends of the light times, when Suryan made the sky glow from horizon to horizon and stars filled the sky when Suryan herself slipped below the edge of the world.But all that has faded with the generations.; Long ago our star melted away into the darkness and we were left clinging to this rock, digging ever deeper into its crust just to reach the feeble warmth of the planet's ancient cooling core.; At least we had that, other colonies were not so lucky.; Those who had settled on artificial planets didn't last long when their stars faded, their power systems were never designed to cope with such extreme cold.; The cold metal constructions lost their heat quickly and their inhabitants (those unlucky enough not to make an escape on whatever ships they might have had) froze in a matter of months.; There are those who say that was a better way to go.Suryan isn't completely dead of course, that takes billions of years.; When she ran out of material to fuse, her outer atmosphere expanded, reaching almost as far as our colony here on the fourth planet.; Protected under the colony's thick-walled domes, the inhabitants watched from safety as the star put on its last and greatest show.; While the core began to shrink, those burnt-orange layers continued to expand, becoming a fading wisp-like shell centred on the dying remains of what had once been a giant nuclear fusion reactor.; That remnant core still sits at the centre of this system like the last dying ember of a fire.; It still produces light and heat of course but not enough to be useful, not by a long way.It's been some decades now since the last ship left this system.; When Suryan burnt its last, up there in the sky, there was widespread panic.; People were desperate to leave, to go somewhere else with a star that was still viable.; But there wasn't anywhere to go.; Slowly but surely, the stars were dying everywhere and there was no more gas left to create new ones.; These are the last days of the Universe, but people refused to believe it.; Somewhere there's another star, they said, somewhere.; The ships left, heading out towards whatever points of light they could see in the sky, and those who stayed behind attempted to carry on as normal.; We've known what was coming for generations but there was nothing we could do.; You either accept it and get on with life as best you can, or panic and most likely hasten your demise.; While we have no ships any more, nor the capabilities to construct any, we can still communicate with other colonies although that happens rarely these days.; There isn't anything left to communicate, and it uses power we can little afford to waste.I often wonder what happened to those ships that left.; The records show that they kept in communication with the colony for some time after they set out, promising to return for survivors when they found a new home in the sunlight.; But then the logs stop.; When I was younger I assumed they just stopped transmitting, that they were saving energy or something.; But now, well, I've heard the stories from other colonies of madness and chaos and I wonder if the same fate befell those ships we dispersed into the night like seeds.That's the problem with space flight of course.; It takes time.; Those ships leaving Suryan would each have headed towards a distant glimmer of light, some far-off star that hadn't yet reached the end of its days.; But in the mean time, the light from those little balls would have been travelling for centuries before it reached our system, if not longer.; What would happen to the crew if, after using all of the fuel they could spare to send them rushing onwards towards some distant star, keeping just enough to slow down again at their intended destination, they suddenly saw that their promised Eden was disappearing, fading away before their very eyes?; By that point there would be nothing they could do, no way of changing course without using up the precious fuel they would need in order to slow down once they reached somewhere habitable.; Game over.; What then?I ask myself: what would I do in that situation?; It would be tempting to open an airlock, destroy the safety interlocks and just let everything be pulled out into the vacuum.; Not a pleasant way to go, certainly, but quicker than most options available on a tug.; We were never an exploration colony, merely a mining outpost, and those craft had never been designed for long-term use.; Your options were starvation (water was recycled, even on the tugs, so no problem there), carbon dioxide poisoning (the filters worked pretty well, but were usually replaced every couple of years), or some manner of your own choosing.; Most colonists would rather chose their way out rather than go slowly - we'd all seen it happen, read the case studies.; It was part of basic schooling on these outposts.; Harsh, may be, but the sooner you realised the realities of colony life the better.So, here lies the remains of a once busy and reasonably prosperous colony.; Mirroring the downfall of the empire, it withered with the dying of the light.; There were those who refused to believe it would happen, others who proclaimed it as the ultimate test of faith in whatever deity they served, still others who maintained that we'd find a way out somehow.; But the truth was that we'd known for generations that this was coming.; Ways of restarting stars were proposed, but they all required more energy than the empire could spare, just for a single star.; Society crumbled, the trade routes grew silent, colonies began shutting off their contact with the outside world.; Where colonies were close enough, wars broke out.The stars didn't all go out at once.; It takes time for a star to use up its fuel, and that depends on many things, but larger stars burn up faster.; Despite the dangers, the empire loved placing colonies around massive stars because they were the most profitable.; You could have several large artificial colonies around a massive star where they could harvest huge amounts of energy, and stellar mechanics was developed enough that the onset of a catastrophic supernova explosion, so characteristic of these massive stars, could be predicted to an accuracy of a few months.; Smaller stars like our Suryan were far more sedate.; Not massive enough to go supernova, they took many billions of years to use up their fuel.; While our colony was never rich, we lasted longer then many others simply because our star was a comparative weakling.But even by the time this colony was founded, the universe was old.; Really, it was a wonder our species had lasted as long as it had without destroying itself from within.; Galaxies formed new stars at the rate of a few per standard solar year, but they have to come from something, you need gas to create them.; No more gas, no more stars.; We knew, as a species, that this was what would happen someday but, like countless cultures before us had done throughout history, we always assumed it would be far enough in the future that it would be someone else's problem.; For the most part that was right, but now we are that someone else, and we are scared.Most of the colony, those who didn't leave in the tugs, have chosen to carry on as normal.; Each year we just dig a bit deeper towards the dying heart of the planet to keep the thermal plants supplied with enough energy from our world's cooling interior.; None of us alive now really knew Suryan as anything other than the dying ember that hangs in the sky today, so to us the sight is normal.; I once saw a holograph of an Earthscape - its open spaces and vivid blue sky were nauseating.; There were no stars in that picture either, apart from Sol of course, now long gone.That's the difference.; Their sky was bright and harsh.; Ours is black and cold, as if oblivion had been given form.; I look out every day at that sky and my eyes wander, searching for the last faint pinpricks of light - something I know I'll never see again, now.; Last night, the last star in our sky faded forever.; We knew it had to happen sometime, but it was still something of a shock when it finally came.; None of us can claim to be astronomers, but we all knew the movements of that last star.; We watched it grow fainter and fainter, occasional bursts of light giving unwarranted hope of a reprieve.; Every one of those upward-gazing eyes knew what those fits meant, but still the soul hopes.... may be.The last star.; The final vestiges of warmth are gone from the sky.; Those photons will continue on, travelling out into the darkness long after this little colony has gone.; For all we know, we may be the last, interstellar communication is a luxury that we can no longer afford.; But what's left now?; There will be no more stars, no more colonies, just endless darkness and cold like the long-dead surface of this planet.There's still time for a walk before lights out.; I've nev... Read more »

Braun, R., Popping, A., Brooks, K., & Combes, F. (2011) Molecular gas in intermediate-redshift ultraluminous infrared galaxies. Monthly Notices of the Royal Astronomical Society, 416(4), 2600-2606. DOI: 10.1111/j.1365-2966.2011.19212.x  

  • September 22, 2011
  • 08:19 PM

Jealousy in an Online World

by eHarmony Labs in eHarmony Labs Blog

Jealousy is a common thing among couples, but what is really causing all these feelings of distress? How does it apply to newer means of communication like online relationships? Read here to find out.... Read more »

  • September 22, 2011
  • 06:23 PM

Can gene therapy eradicate HIV?

by EE Giorgi in CHIMERAS

When I learned about this, my jaw dropped. It almost felt like the old light bulb joke: is it easier to screw in the bulb or to turn the ladder? It turns out, when it comes to HIV, the question is not so ill-posed.HIV infects white cells in our blood called T-cells. It captures a receptor on the cell surface called CCR5, and once it grabs it, it docks with the cell and infects it. T-cells are part of our immune system and they attack the virus as well. Ever since I started working on HIV, the problem, from my end, has been: how can we elicit T-cells and antibodies able to recognize (and destroy) the virus? As I have explained in earlier posts, this has been a challenging task.I've talked extensively about HIV genetic mutations, but, as you know, human genomes carry mutations too. And here's the interesting finding: a mutation called Delta 32 on the CCR5 receptor gene has been identified and linked to a delay in progression to AIDS. In addition, individuals who have both gene copies mutated, are highly resistant to HIV infection [1]. The mutation changes the receptor on the T-cell and in a way that the virus is no longer able to dock with it. And if the virus can't dock with the T-cell, it can't infect it. It slips away until the immune system clears it.So, can we switch the problem around, as in: instead of making T-cells able to recognize the virus, can we make T-cells unrecognizable to the virus?As with many scientific queries, the answer is maybe [2]. In fact, Sangamo BioSciences, a California based company, has an ongoing Phase ½ and two Phase 1 trials using gene therapy to introduce the mutation in HIV infected patients. The Phase 1 trial at the University of Pennsylvania just recently announced that one of the subjects in the study went off the antiretroviral drugs and, after an initial spike, within days viral loads dropped to undetectable.The advantage, if this turns into a permanent eradication of the virus, is the possibility of weaning patients off antiretroviral drugs, which have toxic long term effects and can also develop harmful, drug-resistant strains. Right now HIV infected patients have no choice other than life-long therapy.The flip side is that gene therapy introduces permanent genetic changes and as such, carries risks. There are also numerous caveats (for example, which cells are the best targets), which are thoroughly discussed in [2]. I only have two cautionary comments to add.My first thought is that gene therapy is an expensive and invasive procedure, and even if it does develop into a successful means to defeat the virus, it will unlikely become available to patients in Sub-Saharan Africa. And two thirds of the people currently living with HIV/AIDS are in Sub-Saharan Africa. This is why a vaccine that is not only able to prevent the infection, but also to protect the immune system in case the infection has already started, still remains the best and most affordable option.Second: it's not clear to me whether the results are permanent. You see, HIV is a nasty little virus. It can infect a single cell and stay dormant for years. That is, for years you don't see it, until it wakes up again. And when it wakes up, it can be deadlier than before.   If this "cure" doesn't completely wipe out the virus, it risks of selecting stronger and more resistant strains. HIV replicates so rapidly, and with such a high mutation rate, that it might evolve a new strain able to "grab" the defective receptor. And that would mean a new, tougher viral strain to defeat.[1] Alkhatib G, Combadiere C, Broder CC, Feng Y, Kennedy PE, Murphy PM, & Berger EA (1996). CC CKR5: a RANTES, MIP-1alpha, MIP-1beta receptor as a fusion cofactor for macrophage-tropic HIV-1. Science (New York, N.Y.), 272 (5270), 1955-8 PMID: 8658171[2] Van Lunzen J, Fehse B, & Hauber J (2011). Gene therapy strategies: can we eradicate HIV? Current HIV/AIDS reports, 8 (2), 78-84 PMID: 21331536Photo: wind sculpture, Santa Fe, NM.... Read more »

Alkhatib G, Combadiere C, Broder CC, Feng Y, Kennedy PE, Murphy PM, & Berger EA. (1996) CC CKR5: a RANTES, MIP-1alpha, MIP-1beta receptor as a fusion cofactor for macrophage-tropic HIV-1. Science (New York, N.Y.), 272(5270), 1955-8. PMID: 8658171  

van Lunzen J, Fehse B, & Hauber J. (2011) Gene therapy strategies: can we eradicate HIV?. Current HIV/AIDS reports, 8(2), 78-84. PMID: 21331536  

  • September 22, 2011
  • 06:06 PM

Model predictive control of the hypothalamic-pituitary-adrenal axis

by Jeremy Scheff in Jeremy's Blog

Very recently, I’ve been intrigued by control theory applied to systems biology. This strategy seems to often produce insightful and unintuitive results. In this blog post, I’m going to take a look at a very cool article by Ben-Zvi and coworkers that applies control theory to a mathematical model of the hypothalamic-pituitary-adrenal (HPA) axis, and [...]... Read more »

  • September 22, 2011
  • 05:50 PM

Urban evolution revisited.

by Edmund Hart in Distributed Ecology

Last month I posted about an article in the New York Times on urban ecology and evolution. Since then two interesting papers have come out about natural selection and urban environments. The first is by Halfwerk et al. from PNAS titled: Low-frequency songs lose their potency in noisyurban conditions and a second one also about birds by Rodewald et al. in Ecology: Dynamic selective environments and evolutionary trapsin human-dominated landscapes. Both deal with selective forces that urban environments impose on bird species. Halfwerk et al. worked with Great Tit's Tasty bug! in the Netherlands. Birds that rely on communication via songs have always had to deal with how environments alter their songs, dealing with reverberations in different forest types as an example.Halfwerk et al. examined the affects of anthropogenic noise on female preference for males. Cities typically have low frequency background noise and birds, and in order to cope with this male Great Tit's have change the frequency of their songs to reduce spectral overlap with ambient noise. Halfwerk and colleagues found that males tend to use low frequency songs right before egg laying and that females show higher fidelity when attracted by low frequency songs. But in urban environments there is a rapid signal degradation of the low frequency songs, so if males want to be heard by more females they have to use high frequency songs. The authors argue that this creates a trade-off between natural selection and sexual selection. There is natural selection they argue for high frequency songs because it maintains a strong signal efficiency in urban environments but sexual selection for low frequency songs due to female preference and fidelity. In this study the urban birds are worse off because they are more likely to be cuckolded due to the use of high frequency songs, but in Rodewald et al's work on Cardinals in urban environments the opposite is true. Rodewald et al. examined how urban vs rural environments altered the relationship between plumage coloration and annual reproductive output in the northern Cardinal. They found that Cardinals in urban environments were had no relationship between annual reproductive output and redness (as measured from photographs) but in rural environments there was a negative relationship between redness and reproductive success. Cardinals gain most of their coloration from carotenoids and in typical rural environments these are hard to come by so redness becomes a typical sexually selected trait. Only the strongest cardinals can gain access to the best resources (and carotenoids) and females prefer those cardinals that are the most red. The catch is that in Ohio, where this study took place, there is a common invasive called Amur Honeysuckle (Lonicera maackii). In urban areas this is very common so combined with access to bird food there is no relationship between fitness and redness. In urban environments then there is relaxed sexual selection for coloration. The situation is worse though. In rural environments there is still honeysuckle, but its much more rare and as a consequence the fittest males gain access to it. Red makes me strong!But its what Rodewald calls an "evolutionary trap". Males will choose to nest in it, but its lower to the ground and nests in the honeysuckle are more likely to be preyed upon, especially early in the breeding season. Therefore in rural environments, redness is actually correlated with reduced number of successful reproductions in males. So in this Cardinal system in Ohio, urban birds have an easier time because everybody can be red. One thing that's unclear to me from the study was that I thought if nesting in the invasive honeysuckle causes reduced number of offspring in rural environments, how come urban males don't have the same problem? Regardless of this question though, both studies show how anrthopogenic forces can alter established sexually selective relationships. In the case of the Great Tit's, it was forcing males to change their song to a less desirable one, and in the case of the Cardinal urban environments let every male appear to be a good mate choice. Both studies offer evidence of how urbanization changes the fitness landscapes for organisms. There isn't necessarily anything very novel about this in and of itself, in fact just look at pigeons or house sparrows as examples of birds and urbanization. What's really interesting about both studies is that they show the wide variety of complex interactions that happen with specific facets of urbanization that we rarely consider changing that fitness landscape. What remains to be seen in both systems is what is the eventual upshot of these altered relationships. Will new sexually selective relationships evolve in each species such that there becomes a high degree of "local adaptation" for mating preferences in urban and rural birds? That could be something interesting to study in the future. What are new selective relationships? We can all see the old ones becoming less important because we already know what they are. For instance in the Great Tit its not that females actually prefer high frequency singing males, its just that those are the ones they can find. In fact Halfwerk points out that male-male communication usually uses songs in that frequency range, so will urban environments change bird communication completely then? It would be interesting to see someone make specific predictions about what they expect to see these new relationships would be and to go out and test them. ReferencesHalfwerk W, Bot S, Buikx J, van der Velde M, Komdeur J, Ten Cate C, & Slabbekoorn H (2011). Low-frequency songs lose their potency in noisy urban conditions. Proceedings of the National Academy of Sciences of the United States of America, 108 (35), 14549-54 PMID: 21876157Rodewald, A., Shustack, D., & Jones, T. (2011). Dynamic selective environments and evolutionary traps in human-dominated landscapes Ecology, 92 (9), 1781-1788 DOI: 10.1890/11-0022.1... Read more »

Halfwerk W, Bot S, Buikx J, van der Velde M, Komdeur J, Ten Cate C, & Slabbekoorn H. (2011) Low-frequency songs lose their potency in noisy urban conditions. Proceedings of the National Academy of Sciences of the United States of America, 108(35), 14549-54. PMID: 21876157  

  • September 22, 2011
  • 04:15 PM

Article Review: Animal Play and Animal Welfare

by Austin Bouck in Animal Science Review

Review and discussion of recent article by Held and Spinka.... Read more »

Suzanne D.E. Held, & Marek Spinka. (2011) Animal Play and Animal Welfare. Animal Behaviour, 891-899. info:/

  • September 22, 2011
  • 12:42 PM

Is Lithium a Potential Aid in Traumatic Brain Injury?

by William Yates, M.D. in Brain Posts

Lithium carbonate serves as a primary treatment option in the treatment of mania and bipolar affective disorder.  An elemental metal, lithium has atomic number 3 in the periodic table of elements.The mechanism of action for lithium carbonate in bipolar disorder is unclear.  Some of the proposed mechanisms for lithium in the central nervous system include:alteration of the neurotransmitter glutamate (affected by other drugs linked to therapeutic effect in bipolar disorder, i.e. sodium valproate and lamotrigine)alteration in gene expressioninactivation of the GSK-3B (glycogen synthase kinase) enzyme known to be involved in circadian clock regulationinteraction with the NO (nitrous oxide) signalling pathwayInhibition of the GSK-3B enzyme has been shown to have potential beneficial effects in stimulating neuroplasticity as it is associated with enhanced expression of brain-derived neurotrophic factor (BDNF).  Fengshan Yu and colleagues at NIH and the University of Health Sciences have recently explored the effect of lithium on traumatic brain injury using a mouse model.In their experiment, mice received doses of lithium chloride ranging form 1.0 to 5.0 mEq/kg dose of lithium or placebo following a controlled episode of brain trauma under anesthesia.  Doses were repeated daily for three days.Brain injury response to lithium treatment was monitoring using neuropathological techniques as well as behavior and motor coordination tests.  The key results of the study include:Lithium chloride at 1.5 to 3.0 mEq/kg reduced brain lesion volume compared to controlLithium chloride reduced post-trauma related anxiety behavior during the outcome monitoringLithium chloride reduced breakdown of the blood-brain barriorShort-term and long-term motor coordination was better in the lithium groupThe authors note that their study suggests the neuroprotective effect of lithium administration following traumatic brain injury in the mouse model appears related to a GSK-3B mechanism.  The study timed lithium administration to 3 hours after the trauma providing a realistic model for a trial in human clinical scenarios.  They conclude "Our results that demonstrate its (lithium chloride) benefits in the mouse model pave the way for early clinical trials as potential treatment for TBI (traumatic brain injury) patients.CT of traumatic brain injury showing cerebral contusion, cerebral hemmorhage, subdural hematoma and skull fracture from Wikipedia Creative Commons. Source: Rehman T, Ali R, Tawil I, Yonas H (2008). "Rapid progression of traumatic bifrontal contusions to transtentorial herniation: A case report". Cases journal 1 (1): 203. doi:10.1186/1757-1626-1-203. PMID 18831756. F, Wang Z, Tchantchou F, Chiu CT, Zhang Y, & Chuang DM (2011). Lithium ameliorates neurodegeneration, suppresses neuroinflammation, and improves behavioral performance in a mouse model of traumatic brain injury. Journal of neurotrauma PMID: 21895523... Read more »

  • September 22, 2011
  • 12:12 PM

"Peer-review" does not equal "publisher-owned journal"

by Bradley Voytek in Oscillatory Thoughts

Yesterday was my first real day working at UCSF. Most of it was spent filling out paperwork and completing all of the regulatory training.For those of you unfamiliar with the regulations required for human research, let me just say that they are legion, for they are many. In order to work with human subjects you have to (among other requirements) complete several online courses and questionnaires.This is usually all well and good if not a bit annoying... (Yes, I know I shouldn't inject my subjects with radioactive spider venom without their consent. No, I didn't consider that radioactive spider venom would be an Investigational New Drug. Yes, I disclosed my consultancy income from OSCORP.)Anyway, many universities such as UCSF, Berkeley, etc. require researchers who work with human subjects to complete their online training on a specific website: the Collaborative Institutional Training Initiative. For example I had to complete the "CITI Good Clinical Practice", "Human Subjects Research", and the "Responsible Conduct of Research" curricula. While answering questions in the latter, I encountered the following (which I got "wrong"):(Someone needs to "peer-review" the inconsistant capitalization in the headers and that superfluous comma in that "Comment".)This question struck me as especially odd. "Why," I asked, "is this unscientific, unsubstantiated question here? Are they afraid that researchers will stop publishing their research in peer-revire and just BLOG everything?"Does "those who have an interest in the work" not include peers? Have the authors not heard of course "BLOGS" aren't a replacement for peer-review. Blogs can be peer-reviewed, though, and "peer-review" is not equivalent to a publisher-owned journal. Where does the line between "blog" end and an online journal with commenting begin?As Bora said over at the SciAm blogs:Blog is software. Blog is primarily a platform. It is a piece of software that makes publishing cheap, fast and easy. What one does with that platform is up to each individual person or organization.He points out the open science approach by Rosie Redfield as an example of peer-review that can be moved onto a blog to some extent.Blogs may not replace peer-review, but they are certainly part of it already.As was pointed out in a Nature News piece:To many researchers, such rapid response is all to the good, because it weeds out sloppy work faster. "When some of these things sit around in the scientific literature for a long time, they can do damage: they can influence what people work on, they can influence whole fields," says [David] Goldstein.Personally, I use my blog for many things. I talk about my own research a lot.But I also post some fun, off-the-cuff ideas and analyses that, were I more motivated and had infinite time, I could probably polish and write up for peer-review.It doesn't make those ideas less valuable, just more rough. And I hope someone takes some of them and runs with them. But of course, a major issue here becomes one of idea attribution.As Ben Goldacre said in his Correspondence to Nature:The growth of blogs, Twitter and free online access have caused a welcome explosion in scientific content. But this is atomized and interconnected by a hotchpotch of linking and referencing conventions. If we are going to harness its true value, we shall need dedicated librarians and information scientists to find ways of automating the process of linking content together again. That in itself would be a transgressive scientific innovation.The current academic reward structures don't give me anything for this blog. So in the meantime I'll continue doing research with people and publishing it in "real" peer review while rolling my eyes at the occasional awkwardness with which academia approaches technology.Goldacre, B. (2011). Harnessing value of dispersed critiques Nature, 470 (7333), 175-175 DOI: 10.1038/470175bMandavilli, A. (2011). Peer review: Trial by Twitter Nature, 469 (7330), 286-287 DOI: 10.1038/469286a... Read more »

Goldacre, B. (2011) Harnessing value of dispersed critiques. Nature, 470(7333), 175-175. DOI: 10.1038/470175b  

Mandavilli, A. (2011) Peer review: Trial by Twitter. Nature, 469(7330), 286-287. DOI: 10.1038/469286a  

  • September 22, 2011
  • 12:09 PM

The ritual boundaries of household worship

by Nikolaos Markoulakis in Tropaion

In between two columns that represent
the interior of an oikos
stands a woman, reaching to an altar;
a wreath is hung on the wall behind her.
A scene comparable with Menanders
discription of a domestic ritual boundary.
Musée du Louvre CA 1857. © Perseus 1992
For a number of brief posts, the past six years, I discussed elements of the commonly known 'household' worship, supported with

... Read more »

John Pedley. (2005) Sanctuaries and the Sacred in the Ancient Greek World. Cambridge University Press. info:/10.2277/052100635X

  • September 22, 2011
  • 11:59 AM

I Can't Get No Job Satisfaction

by Duncan Hull in O'Really?

Job satisfaction is like a complex mathematical equation that needs to be balanced. There are many factors that contribute to the mix, both good and bad. Hopefully the good things about a job will outweigh the bad. But what are the good things that contribute to the elusive but crucial job satisfaction?... Read more »

Ariely, D., Gneezy, U., Loewenstein, G., & Mazar, N. (2009) Large Stakes and Big Mistakes. Review of Economic Studies, 76(2), 451-469. DOI: 10.1111/j.1467-937X.2009.00534.x  

  • September 22, 2011
  • 11:48 AM

Commodity Traitors: Financial Speculation on Commodities Fuels Global Insecurity

by Eric Michael Johnson in The Primate Diaries

“Food is always more or less in demand,” wrote Adam Smith in The Wealth of Nations. While the founder of modern capitalism pointed out that the wealthy consume no more food than their poor neighbors, because the “desire of food is limited in every man by the narrow capacity of the human stomach,” the desire [...]

... Read more »

Marco Lagi, Yavni Bar-Yam, Karla Z. Bertrand, & Yaneer Bar-Yam. (2011) The Food Crises: A quantitative model of food prices including speculators and ethanol conversion. New England Complex Systems Institute. info:/

  • September 22, 2011
  • 10:00 AM

Unfolding the IKEA Effect: Why We Love the Things We Build

by Richard Landers in NeoAcademic

The IKEA Effect refers to the tendency for people to value things they have created/built themselves more than if made by someone else – in fact, nearly as much as if an expert had created the same item.  I recently came across a fascinating article by Norton, Mochon and Ariely[1] in the Journal of Consumer [...]

Related articles from NeoAcademic:Stats and Methods Urban Legend 4: Effect Size vs. Hypothesis Testing
Those Auditors Love Second Life
Predicting Dropout Rates for Students Completing Online Surveys
Stats and Methods Urban Legend 2: Control Variables Improve Your Study
... Read more »

Norton, M., Mochon, D., & Ariely, D. (2011) The IKEA effect: When labor leads to love. Journal of Consumer Psychology. DOI: 10.1016/j.jcps.2011.08.002  

  • September 22, 2011
  • 09:40 AM

What Influences Our Conformity to Social Norms?

by Eric Horowitz in peer-reviewed by my neurons

One of the great trials and tribulations of human existence is that it’s hard to get other people to do want you want.  Fortunately, most people manage to conform to at least two different types of social norms. Injuctive norms reflect behaviors chosen because people perceive them be correct — for example, not throwing trash [...]... Read more »

  • September 22, 2011
  • 09:25 AM

Careful, Your Animation May Be Promoting Hindsight

by Dr. Ken Broda-Bahm in Persuasive Litigator

Standing in front of a legal fact-finder you need to visually persuade and you also need to defeat the psychological biases that can harm your case. But here is a terrible thought: What if one of the best tools of visual persuasion has the unintended side-effect of promoting an often-harmful psychological bias? Well, the bad news according to recent studies is it does. This post takes a look at the research, as well as the recommendations on creating animations that teach without biasing. ... Read more »

Florian Fessel and Neal J. Roese. (2011) Hindsight Bias, Visual Aids, and Legal Decision Making: Timing is Everything. Social and Personality Psychology Compass , 5(4), 180-193. info:/

  • September 22, 2011
  • 09:14 AM

Degeneracy, Evolution and Language

by Wintz in A Replicated Typo 2.0


Having had several months off, I thought I’d kick things off by looking at a topic that’s garnered considerable interest in evolutionary theory, known as degeneracy. As a concept, degeneracy is a well known characteristic of biological systems, and is found in the genetic code (many different nucleotide sequences encode a polypeptide) and immune responses (populations . . . → Read More: Degeneracy, Evolution and Language... Read more »

  • September 22, 2011
  • 09:00 AM

Using Tweets to Predict Box Office Success #stratfest #broadway

by Anatoliy Gruzd in Social Media Lab

Does the number of tweets a theatrical production receives correlate with its success, and can the tweets be used to predict a production’s popularity? In May I began a study examining the Stratford Shakespeare Festival’s use of Twitter. Over the past several months I have been using Netlytic, a web-based system being developed here at [...]... Read more »

The Really Useful Group. (2011) Andrew on the Stratford Festival production of Jesus Christ Superstar. Blog post. info:/

  • September 22, 2011
  • 07:00 AM

September 22, 2011

by Erin Campbell in HighMag Blog

I love it when worlds collide. I love the movies where a country boy falls for a city girl. Or a robot develops a friendship with a wookie. Hilarity typically ensues in the movies, but fantastic new ideas and questions result from the discovery of biological processes colliding. So, when I came across a recent paper that revealed new results on the relationship between endocytosis and adhesion, I was all over it. Cell-cell adhesion is constantly adjusted throughout development, wound healing, and cancer metastasis. E-cadherin is the major adhesion molecule that functions in epithelial cell adhesion and polarity, and is linked to the actin skeleton (via α-catenin) and p120. The level of E-cadherin at the cell surface influences the adhesive strength between two cells, and this strength can be adjusted by internalization (endocytosis) of E-cadherin away from the cell surface. A recent paper discusses results showing how internalization of E-cadherin is regulated by Numb, a protein that interacts with endocytosis adaptor proteins and is important throughout development. Sato and colleagues found that Numb interacts directly with p120, and showed that impairment of Numb prevents E-cadherin internalization. The images above show cysts of epithelial cells. In control cysts (top rows), E-cadherin and p120 (red) were found at the basolateral cell-cell junctions. In cysts with reduced levels of Numb (bottom rows), both E-cadherin and p120 localized to the apical membrane region (blue) too.Sato, K., Watanabe, T., Wang, S., Kakeno, M., Matsuzawa, K., Matsui, T., Yokoi, K., Murase, K., Sugiyama, I., Ozawa, M., & Kaibuchi, K. (2011). Numb controls E-cadherin endocytosis through p120 catenin with aPKC Molecular Biology of the Cell, 22 (17), 3103-3119 DOI: 10.1091/mbc.E11-03-0274... Read more »

Sato, K., Watanabe, T., Wang, S., Kakeno, M., Matsuzawa, K., Matsui, T., Yokoi, K., Murase, K., Sugiyama, I., Ozawa, M.... (2011) Numb controls E-cadherin endocytosis through p120 catenin with aPKC. Molecular Biology of the Cell, 22(17), 3103-3119. DOI: 10.1091/mbc.E11-03-0274  

  • September 22, 2011
  • 06:30 AM

Students don't lose their ability to think scientifically

by Marie-Claire Shanahan in Boundary Vision

Taking a critical look at assertions that children are natural scientists who lose their abilities as they mature.... Read more »

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