Post List

  • July 7, 2011
  • 09:36 PM

A Language of Light from a Tiny Molecule

by Dan Bailey in Smells Like Science

As a little kid I was an expert firefly catcher. But these days, I’m clearly out of practice. I spent a good half-hour the other night unsuccessfully chasing down fireflies to photograph for this post. As soon as they stopped glowing they receded into the darkness, becoming nearly invisible. Eventually I gave up the hunt and watched the seemingly random flickers of light coming from the fireflies all around me. What looks at first glance like random sparks and flashes in the night, is actually an intricate, flirtatious conversation between male and female fireflies.... Read more »

  • July 7, 2011
  • 08:19 PM

Ketones and environmental toxicity

by Lucas Tafur in Ketotic

A ketogenic diet protects from soman toxicity. ... Read more »

  • July 7, 2011
  • 06:00 PM

English monkey gives itself a pedicure with self-made tools

by Ed Yong in Not Exactly Rocket Science

Animals use tools to get food, communicate with one another, defend themselves or even have a scratch. But in Chester Zoo, England, one monkey uses tools to give itself a pedicure.
Riccardo Pansini and Jan de Ruiter from Durham University watched a 18-year-old mandrill called JC clean his toenails out using small splinters. He made them himself, fashioning them from wood chips and twigs on the floor his enclosure, and honing them till they were small and sharp.
JC is the alpha male of the zoo’s six-strong group of mandrills. Over three months of observations, Pansini and de Ruiter saw JC give himself a pedicure seven times. On a couple of occasions, he ignored the wood altogether and just plucked out one of his own hairs to clean his nails with.
Many animals will use tools, but it’s not often that they modify those tools to make them more suitable for their needs. Chimps do it, as do New Caledonian crows. Among monkeys, biologists have documented a capuchin dressing her baby’s head wound with modified plants, spider monkeys making back-scratchers out of sticks, and Japanese macaques ...... Read more »

  • July 7, 2011
  • 04:30 PM

Bizarro World at the World Congress of Physical Therapy

by Lorimer Moseley in BodyInMind

The World Congress of Physical Therapy was a bit like Bizarro world for me. Steven Kamper, provided a great post summarizing the conference, but I wanted to build on it a little. ... Read more »

  • July 7, 2011
  • 04:18 PM

Brown-Lipped Snails

by Africa Gomez in BugBlog

The Brown-lipped or Grove snail, Cepaea nemoralis has received a lot of attention by evolutionary biologists for more than a century, due to their strikingly variable shell colour - what is called colour polymorphism. In the decades of the middle of the last century it was a very popular research organism. The shiny shell can be yellow, pink or brown. Over each of these background colours there can be no bands, one band or five bands, and the bands can also be fused and be of variable width. The snail above, which we found yesterday feeding on the fallen leaves on the garden path, is a yellow/one banded one. This polymorphism happens within the same population, but what puzzled biologists was the occurrence of sharp changes in the frequency of colour forms from one population to the next, and these differences seem to persist with time. This phenomenon was called "area effects". Many explanations have been proposed through the years to explain how the polymorphism is maintained and how area effects come to be, from differential predation (especially by song thrushes), adaptation to microhabitat, or other forms of selection to chance effects due to colonization after the glaciations, genetic linkage, dispersal between populations, etc. Many of these factors are not mutually exclusive and seem to have different importance depending on the population. We found the shells below in the beach in Spurn Head a few years ago, all in a small area. They are a bit bleached by the sun, but you can see yellow and pink snails and three types of banding patterns.The Brown Lipped snail can be found from dunes to roadsides, gardens and closed woodland. It can live up to 8 years old. They prefer to feed on dead vegetation than fresh, and on average, only 9% of its diet is fresh vegetation, although this percentage can increase during dry spells.ReferencesCain AJ, & Sheppard PM (1954). Natural Selection in Cepaea. Genetics, 39 (1), 89-116 PMID: 17247470Davison, A., & Clarke, B. (2000). History or current selection? A molecular analysis of 'area effects' in the land snail Cepaea nemoralis Proceedings of the Royal Society B: Biological Sciences, 267 (1451), 1399-1405 DOI: 10.1098/rspb.2000.1156Paul J. Mensink & Hugh A. L. Henry (2011). Rain event influence short-term feeding preferences in the snail Cepaea nemoralis Journal of Molluscan Studies. DOI: 10.1093/mollus/eyr011... Read more »

Cain AJ, & Sheppard PM. (1954) Natural Selection in Cepaea. Genetics, 39(1), 89-116. PMID: 17247470  

Paul J. Mensink . (2011) Rain event influence short-term feeding preferences in the snail Cepaea nemoralis. Journal of Molluscan Studies. info:/10.1093/mollus/eyr011

  • July 7, 2011
  • 03:32 PM

Science Translational Medicine on Innovation – part 1

by Pieter Droppert in Biotech Strategy Blog

With an image of Rodin’s bronze “The Thinker” on its cover suggesting deep thought and insight, Science Translational Medicine (STM) analyzes the state of innovation in its June 29 issue. STM states (without any authority) that “A powerful perception that … Continue reading →... Read more »

Edelman, E., & Leon, M. (2011) The Fiber of Modern Society. Science Translational Medicine, 3(89), 89-89. DOI: 10.1126/scitranslmed.3002190  

  • July 7, 2011
  • 03:00 PM

Cassini helps us peek underneath the surface of Enceladus

by Kelly Oakes in Basic Space

The Cassini spacecraft is zooming around Saturn as I type, currently in between two flybys of Saturn’s moon Titan – one was in June, the next will be September. It was supposed to explore Saturn and its moons for only four years between 2004 and 2008.... Read more »

  • July 7, 2011
  • 01:00 PM

Taking Bugs Out For a Spin

by Moselio Schaechter in Small Things Considered

by Linh Truong and Shabana Din

Microbes are the most robust of all life forms inhabiting our planet. Their ability to proliferate in extreme temperatures, pH, pressure, and radiation is well documented. They not only withstand but grow at physical extremes, which makes us wonder about the physical bounds for life not...... Read more »

Deguchi S, Shimoshige H, Tsudome M, Mukai SA, Corkery RW, Ito S, & Horikoshi K. (2011) Microbial growth at hyperaccelerations up to 403,627 x g. Proceedings of the National Academy of Sciences of the United States of America, 108(19), 7997-8002. PMID: 21518884  

  • July 7, 2011
  • 12:32 PM

The Tools of the Human Microbiome

by Rob Mitchum in ScienceLife

The latest cult favorite in the sphere of human genetics is the microbiome, the genes of the bacterial species that live inside and upon the human body. Because bacterial cells outnumber human cells in an adult by approximately ten to one, and tens of thousands of different species make up the human ecosystem, studying this [...]... Read more »

  • July 7, 2011
  • 12:10 PM

The Princess on the Pea – Mechanisms of Chronic Pain

by Kim Kristiansen in Picture of Pain

Today we have a pretty good knowledge of the mechanisms behind chronic pain. This is a presentation of the basic understanding of how chronic pain starts, what causes it and why we most often are not able to see it on x-ray, MRI or other diagnostic procedures despite the fact that the patient are experiencing pain. We comes around allodynia, hyperalgesia, sensitization regulatory pathways and influence of sleep, depression and much more.

We also take a look on what could be wrong with “The Princess on the Pea” ….... Read more »

Kim Kristiansen. M.D. (2011) The Princess on the Pea – Mechanisms of Chronic Pain. Picture of Pain Blog. info:/

  • July 7, 2011
  • 12:10 PM

On human health, interesting the public, and good scientific journalism...

by Heather in Escaping Anergy: The Immunology Research Blog

In addition to the "pulled from the scientific journal headlines" research discussed here, I thought it would be interesting to periodically showcase fascinating research that I read elsewhere. Awesome and interesting research about human health, disease and immunology is everywhere and sometimes, it's written about in a way that is clear, accurate and easy to understand! That last point is exactly what Escaping Anergy is all about: a place to see, interpret, discuss and most importantly-UNDERSTAND- the scientific data behind the science stories we read about, the diseases we encounter and the medicines we take! Today's topic: how the wavelength of light we see affects our immune system and cancer progression.
... Read more »

Cajochen C, Frey S, Anders D, Späti J, Bues M, Pross A, Mager R, Wirz-Justice A, & Stefani O. (2011) Evening exposure to a light-emitting diodes (LED)-backlit computer screen affects circadian physiology and cognitive performance. Journal of applied physiology (Bethesda, Md. : 1985), 110(5), 1432-8. PMID: 21415172  

  • July 7, 2011
  • 12:00 PM

Shifting Stigmas: The Act of Crying in Public

by Krystal D'Costa in Anthropology in Practice

Jimmy Dugan firmly established that there’s no crying in baseball. But what about in public? In New York City, at some point or another you’re going to encounter a crying person—in fact, you could even be the crier. A few weeks ago, I boarded the subway for a short trip uptown. It was the middle [...]

... Read more »

Borgquist, Alvin. (1906) Crying. The American Journal of Psychology, 17(2), 149-205. info:/

Ross, C., & Mirowsky, J. (1984) Men Who Cry. Social Psychology Quarterly, 47(2), 138. DOI: 10.2307/3033942  

  • July 7, 2011
  • 11:15 AM

The Saga on Fat Continues

by Brooke N in Smaller Questions

It turns out there is one more reason extra fat in our diet just isn’t good for you – excess fat can trigger cell suicide. Recently, Jean Schaffer’s group at Washington University have identified a very special RNA that responds to excess fat in the cell.... Read more »

Michel CI, Holley CL, Scruggs BS, Sidhu R, Brookheart RT, Listenberger LL, Behlke MA, Ory DS, & Schaffer JE. (2011) Small Nucleolar RNAs U32a, U33, and U35a Are Critical Mediators of Metabolic Stress. Cell metabolism, 14(1), 33-44. PMID: 21723502  

  • July 7, 2011
  • 11:08 AM

More Time In Bed Boosts Basketball Performance

by William Yates, M.D. in Brain Posts

Looking for that extra edge on the basketball court?  Want to increase your free throw percentage and gain an extra step in quickness?  Is it a new performance enhancing drug or training technique?  No, a new study suggests it may be as easy as spending a few extra hours in bed. Cheri Mah and colleagues from Stanford University and the University of California, San Francisco recently published their research on sleep and athletic performance in the journal Sleep.  They introduce the study by noting that extensive research documents the adverse effect of limited sleep.  However, little research examines the effect of increased sleep on performance.  Their study objective was to do just that. Members of the Stanford University mens basketball team were recruited for the study.  The study took place over two seasons and included a baseline period of usual sleep patterns.  Then the intervention group extended their sleep pattern with a goal of a minimum of 10 hours in bed daily. Compliance with this intervention was measured through sleep journals and actigraphy.  Actigraphy is accomplished by a wrist device that is worn and measures movement.  From this data the total sleep time can be estimated.  Sleep journal data and activity data estimated the increase in total daily sleep time to be between 100 and 150 minutes of additional sleep during the intervention period.Athletes in the intervention groups were tested on a variety of psychometric and basketball performance skills during the baseline and intervention period.  The results of the intervention were pretty impressive.  Here is a summary of the improvement noted in the study:Free throw percentage increased by 11%Three point percentage increased by 14%Sprint test time decreased by 4%Other psychometric variables were improved including a reduction in time on the Psychomotor Vigilance Task, a reduction in the Epworth Sleepiness Scale score and improvement on multiple components of the Profile of Mood States including ratings of fatigue, depression and tension.The authors note the study has some significant limitations in research design.  Only eleven athletes received the intervention.  Subjects were not blinded as to the intervention and it is possible a some of the improvement came from an expectancy effect.  Travel schedules made it difficult to assure compliance with the 10 hours in bed intervention for every day of the study.However, this study does suggest that many athletes may be performing in the context of ongoing sleep deprivation.  Forcing compliance with an extended sleep duration holds promise of improving performance on the basketball court.  This effect appears to occur in the context of subjective improvement in psychological function.If I were an NCAA basketball athlete, I would send a copy of this study to my coach and training staff.  Athletes now have some research to support the importance of getting plenty of sleep to achieve peak performance.Photo of Oklahoma City Thunder Player Blake Griffin Shooting Free Throw Courtesy of Tim YatesMah CD, Mah KE, Kezirian EJ, & Dement WC (2011). The Effects of Sleep Extension on the Athletic Performance of Collegiate Basketball Players. Sleep, 34 (7), 943-950 PMID: 21731144... Read more »

  • July 7, 2011
  • 10:43 AM

How do life events affect body weight? Part 2

by pennydeck in Feedback Solutions for Obesity

In my previous blog post, I discussed a paper by Ogden and Hills (1) that explores individuals’ perceived triggers of behaviour change and the factors that contribute to maintaining behaviour change over time. But a number of questions remain: are … Continue reading →... Read more »

  • July 7, 2011
  • 09:00 AM

Does Neuronal Scarring Determine the Body Weight Set Point?

by Arya M. Sharma in Dr. Sharma's Obesity Notes

As regular readers are well aware, one of the major dilemmas in obesity management is the fact that virtually any attempt at weight loss is counteracted by complex mechanisms that aim to restore the body back to initial weight.
So far, no one has discovered a way to reverse or ‘reset’ this mechanism so that, once [...]... Read more »

Horvath TL, Sarman B, García-Cáceres C, Enriori PJ, Sotonyi P, Shanabrough M, Borok E, Argente J, Chowen JA, Perez-Tilve D.... (2010) Synaptic input organization of the melanocortin system predicts diet-induced hypothalamic reactive gliosis and obesity. Proceedings of the National Academy of Sciences of the United States of America, 107(33), 14875-80. PMID: 20679202  

  • July 7, 2011
  • 08:00 AM

Vaccine Confidence: Attitudes and Actions

by Scott Gavura in Science-Based Medicine

Few groups are more hazardous to public health than the anti-vaccine movement – because there’s a body count affiliated with their actions. When vaccination rates drop, communicable diseases re-emerge, and people suffer. While anti-vaccine sentiment will probably persist as long as vaccines are around, we’re fortunate that vaccination rates, on balance, remain very high. In [...]... Read more »

Kennedy A, Lavail K, Nowak G, Basket M, & Landry S. (2011) Confidence about vaccines in the United States: understanding parents' perceptions. Health affairs (Project Hope), 30(6), 1151-9. PMID: 21653969  

  • July 7, 2011
  • 07:45 AM

Men are as motivated by cute baby faces as women

by BPS Research Digest in BPS Research Digest

Cuteness as an evolutionary adaptation
Both Charles Darwin and Konrad Lorenz, the pioneering ethologist, wrote about the appeal of baby faces as a possible adaptive mechanism. They surmised that babies' perceived cuteness could be nature's way of ensuring the little terrors get looked after. Now a team led by Morten Kringelbach and Christine Parsons has shown that men are as motivated by baby faces as women. Kringelbach is the same researcher who a few years ago showed that looking at baby faces, as opposed to adult faces, is associated with a distinct pattern of brain activity in the orbitofrontal cortex - a kind of neural "cuteness response".

For the new study, 31 men and 37 women (average age 20 years), all with limited experience of babies, looked at photographs of the faces of 70 babies (aged 3 to 12 months), each shown for five seconds, and rated their attractiveness. These results conformed to cultural stereotypes about gender differences, with the women tending to rate the babies as more attractive than the men (no such gender difference emerged for the rating of adult faces). A desire to conform to gender roles could have played a role here. However, both men and women rated as more attractive those baby faces that most closely conformed to the cute ideal: a large rounded forehead, large low-set eyes, a short and narrow nose and a small chin.

In another part of the experiment, performed either before or after the attractiveness ratings, the participants were able to press a button repeatedly to control how long each baby face remained on the screen. This was taken as a measure of how much the participants were motivated to look at the faces. In this case the men scored just the same as the women. Moreover, for both men and women it was those faces that most closely conformed to the cute ideal that they made the effort to look at for longer.

"Our findings indicate that both men and women appraise what is colloquially described as a 'cute' unfamiliar infant positively, and they will work to see that infant for longer than an infant with less 'cute' features," the researchers said. "This is in line with previous studies showing that 'cuter' infants are rated as more friendly, cheerful, and likeable and are rated as more 'adoptable'."

Parsons, C., Young, K., Kumari, N., Stein, A., and Kringelbach, M. (2011). The Motivational Salience of Infant Faces Is Similar for Men and Women. PLoS ONE, 6 (5) DOI: 10.1371/journal.pone.0020632

This post was written by Christian Jarrett for the BPS Research Digest.

... Read more »

  • July 7, 2011
  • 07:33 AM

more on auto metaphor recognition methods

by Chris in The Lousy Linguist

A quick follow-up to my previous post on automatic metaphor recognition. The paper Automatic Metaphor Recognition Based on Semantic Relation Patterns by Tang et al. challenges the dominant selectional preferences method by substituing their own Semantic Relations Patterns. They point out the problems with Selection Preferences (unfortunately I don't think they solved the problems with their own method, more on that in a bit).Again I'll give the Ling 101, computational linguistics for dummies version (as I understand it ...): Selection Preferences assumes that words frequently co-occur with other words that are literally associated with the same semantic domain. For example,That ship has sailed the mighty ocean.That boat has sailed across lake Erie.That captain has sailed many seas.In these three sentences, the verb sailed occurs with three different subjects (ship, boat, captain) and three different objects (ocean, lake, seas), but all of them evoke the SAILING domain. So a computer could use this info to create a model of the verb sail that would match up the semantics of its expected subjects and objects, then compare them to a new sentence. If the computer encountered the new sentence    4. That student sailed through final exams.It could automatically use the model created from sentences 1-3 above to recognize that the verb sailed occurs with a subject and object not from the SAILING domain, but rather from the STUDENT domain. Then it could use a metaphor mapping component to recognize that HUMANS as MACHINES is an acceptable mapping and thus recognize that #4 might be coherent under a metaphorical interpretation.Tang et al. rightly point out that matching frequency-based selectional preferences is not the same thing as literal meaning. First, they note that some times, a metaphorical pairing is actually MORE FREQUENT than a litertal pairing. They use some Chinese examples, but I think the English translation makes the point. Take the following two uses of close:The plane is close to the tower.Opinion are close.In their corpus, Chinese uses like 'opinions are close' were more frequent, even though this is a non-literal use of close. Frequency would lead the Selectional Preference method to believe that the opinions-type use is literal simply because it is more frequent. This outcome is predicted by Lakoff & Johnson, btw, because one of the core tenants of their seminal work on metaphors was that metaphors are NOT special uses of language, but rather quite common and normal.Tang et al.'s solution is a new method they call Semantic Relation Patterns. Their explanation is brief and highly technical, making it a slog to get through, but it hinges on incorporating an existing semantic relations knowledge base, HowNet, and adding a probabalistic model. Note, I had trouble getting the HowNet website to load, but here is a PDF explanation.How Net is an on-line common-sense knowledge base unveiling inter-conceptual relations and inter-attribute relations of concepts as connoting in Chinese and English bilingual lexicons. In my quick read the two methods differed only minimally in the crucial ways (namely, they are both lexalist and local). Semantic Relation patterns are still based on lexical semantics and still derived entirely locally. I don't see how SRP would handle this metaphor from my earlier post any better than SP:Imagine a situation in a biology class where two students, Alger and Miriam, were originally going to be partners for a lab assignment. Then they got into an argument. A third student, Annette, asks Miriam:Annette: Are you still going to be lab partners with Alger?Miriam: No. That ship has sailed.In this scenario, the sentence "That ship has sailed" is entirely coherent from a selectional preferences perspective (i.e., ships really do sail). Yet it is clearly being used metaphorically (there is literally no ship). Here, the metaphor is only detectable if we link two sentences together via co-reference. The phrase "the ship" does not co-refer to a real ship in the discourse. Rather, it refers to the possible event of be-lab-partners-with-Alger. Unless we can link phrases between sentences and between types (i.e., allowing an NP to co-refer to an event), then we are not going to get a computer to recognize these types of metaphors (which I suspect are quite common).I appreciate Tang et al.'s critique of the SP method and their attempt to get beyond it, but I think their methodology fails to make the critical improvements to automatic metaphor recognition that will be crucial to creating a full scale tool that handles real world metaphor.Xuri Tang, Weiguang Qu, Xiaohe Chen, & Shiwen Yu (2010). Automatic Metaphor Recognition Based on Semantic Relation Patterns International Conference on Asian Language Processing... Read more »

Xuri Tang, Weiguang Qu, Xiaohe Chen, & Shiwen Yu. (2010) Automatic Metaphor Recognition Based on Semantic Relation Patterns. International Conference on Asian Language Processing. info:/

  • July 7, 2011
  • 07:00 AM

July 7, 2011

by Erin Campbell in HighMag Blog

Totally tubular! If Bill and Ted had an excellent adventure in the human body, you can be certain that they’d learn about the most excellent tube structures throughout the body. From the veins that carry our blood to the branching tubules in our lungs, tubes are very important structures. A recent paper looks at the role of adhesion proteins during tubule formation.During development, dramatic rearrangements of epithelial sheets results in the formation of branched tubules, as seen in kidney, lung, and mammary gland tissue. As one might expect, these rearrangements require coordination of several cellular events such as cell division, migration, polarization, and adhesion. A recent paper describes the role of two adhesion proteins, E-cadherin and cadherin-6, in tubule formation. Jia and colleagues found that cadherin-6 is important in inhibiting tubule formation, while E-cadherin is important in the formation of a tubule’s lumen (its inside cavity). Images above show the use of cell cysts as a model for epithelial tubule and lumen formation, with fluorescent tags showing a lateral marker (blue) and lumen-facing apical markers (green and red). Samples of control cysts, cysts without cadherin-6, E-cadherin, or both are shown (moving left to right). Although the mutant cysts appear abnormal, polarization was not disrupted in cysts without either cadherin (although multiple lumens are visible in cysts lacking E-cadherin). The polarization of cysts lacking both cadherins, however, was completely disrupted.Jia, L., Liu, F., Hansen, S., ter Beest, M., & Zegers, M. (2011). Distinct roles of cadherin-6 and E-cadherin in tubulogenesis and lumen formation Molecular Biology of the Cell, 22 (12), 2031-2041 DOI: 10.1091/mbc.E11-01-0038... Read more »

Jia, L., Liu, F., Hansen, S., ter Beest, M., & Zegers, M. (2011) Distinct roles of cadherin-6 and E-cadherin in tubulogenesis and lumen formation. Molecular Biology of the Cell, 22(12), 2031-2041. DOI: 10.1091/mbc.E11-01-0038  

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