Post List

  • May 30, 2011
  • 06:09 AM
  • 1,169 views

A critical point in QCD exists indeed!

by Marco Frasca in The Gauge Connection

After my comeback from the conference in Ghent (see here, here and here), I started a collaboration with Marco Ruggieri. Marco was instrumental in making me aware of that part of the community that does computations in QCD at finite temperature. The aim of these people is to get a full landscape of the ground [...]... Read more »

T. Hell, S. Roessner, M. Cristoforetti, & W. Weise. (2008) Dynamics and thermodynamics of a nonlocal Polyakov--Nambu--Jona-Lasinio model with running coupling. Phys.Rev.D79:014022,2009. arXiv: 0810.1099v2

D. Gomez Dumm, & N. N. Scoccola. (2004) Characteristics of the chiral phase transition in nonlocal quark models. Phys.Rev. C72 (2005) 014909. arXiv: hep-ph/0410262v2

  • May 30, 2011
  • 06:00 AM
  • 1,121 views

Article review: Improving case presentations with theater training

by Michelle Lin in Academic Life In Emergency Medicine

"To be or not to be?"What could be more strange on a medical school curriculum than a theater training course? The authors of this study in Medical Humanities innovatively designed a 1-week elective course to help medical students at Mayo Medical School to improve their case presentation skills in partnership with the Guthrie Theater.In this pilot course, seven medical students (six 1st year students, one 4th year student) participated. The learning objectives were:Hear stories: those told by patients, colleagues and in written narrativesIdentify the elements of a narrative, and examine stories for narrative structure Share stories: through case presentations, body movement, storytelling and acting Present a patient’s story with elements of traditional medical presentation and narrativeStudents were evaluated for the following competencies:The cognitive capacity and flexibility needed to evaluate and acquire reliable clinical information. ... Read more »

Hammer RR, Rian JD, Gregory JK, Bostwick JM, Barrett Birk C, Chalfant L, Scanlon PD, & Hall-Flavin DK. (2011) Telling the Patient's Story: using theatre training to improve case presentation skills. Medical humanities, 37(1), 18-22. PMID: 21593246  

  • May 30, 2011
  • 06:00 AM
  • 1,031 views

Article review: Improving case presentations with theater training

by Michelle Lin in Academic Life In Emergency Medicine

"To be or not to be?"What could be more strange on a medical school curriculum than a theater training course? The authors of this study in Medical Humanities innovatively designed a 1-week elective course to help medical students at Mayo Medical School to improve their case presentation skills in partnership with the Guthrie Theater.In this pilot course, seven medical students (six 1st year students, one 4th year student) participated. The learning objectives were:Hear stories: those told by patients, colleagues and in written narrativesIdentify the elements of a narrative, and examine stories for narrative structure Share stories: through case presentations, body movement, storytelling and acting Present a patient’s story with elements of traditional medical presentation and narrativeStudents were evaluated for the following competencies:The cognitive capacity and flexibility needed to evaluate and acquire reliable clinical information. ... Read more »

Hammer RR, Rian JD, Gregory JK, Bostwick JM, Barrett Birk C, Chalfant L, Scanlon PD, & Hall-Flavin DK. (2011) Telling the Patient's Story: using theatre training to improve case presentation skills. Medical humanities, 37(1), 18-22. PMID: 21593246  

  • May 30, 2011
  • 05:30 AM
  • 1,622 views

Are we obese 'cause we sit all day long?

by Yoni Freedhoff in Weighty Matters

That was one of the cases put forth by Dr. Bob Ross during our Forks vs. Feet debate.He had discussed an as of then unpublished study that concluded that due to changes in occupation-based physical activity, we were all on average burning 100 fewer calories per workday, and that those no longer burned calories have caused us to become obese.Well, the paper was just published and I had a gander.Now I do think there are weaknesses to the analysis, in that this study of theoretical energy expenditure lost at work doesn't in fact provide a picture of total daily energy expenditure. Meaning that the authors have no idea what the study subjects energy expenditures were like when they weren't working. That's problematic for a few reasons.Firstly it's problematic because it's possible that if you take away 100 calories burned through physical labour, perhaps you'll put them back elsewhere. What I mean to say is that in children we've seen evidence for the existence of an Activitystat whereby kids who exercise more at school do less at home and vice-versa. Given such behaviour has been demonstrated to exist in children, I don't think it's an impossible stretch to wonder if it also occurs in adults, especially since we're talking about just 100 calories per day. And even if it didn't translate to intentional exercise, couldn't more sedentary jobs lead to more fidgeting? More fidgeting would mean more Non-Exercise Activity Thermogenesis. Dr. Levine suggests purposeful NEAT can add up to 500-1000 calories a day, how difficult would an unconscious 100 be?Secondly it's problematic because doubly-labeled water studies suggest that at least between 1983 and 2005, in study populations from Holland and North America, daily energy expenditures haven't changed. Yet in both Holland and North America during that same time period obesity rates have risen dramatically and presumably, we're working progressively cushier jobs.Thirdly it's problematic because in doubly labeled water studies that look at total daily energy expenditure of folks living in developing nations vs. developed nations, for instance subsistence farmers in Nigeria vs. urban Chicagoans, there's been no difference in calories burned, and that total daily calories burned in both populations didn't correlate with weight. I would certainly imagine that being a subsistence farmer in Nigeria would be quite physically demanding work. Lastly, in a massive study of 98 doubly labeled water studies representing 183 cohorts including 14 from countries with low or middle "human development index" (and hence more likely to have physically demanding jobs), again there was no difference in total daily energy expenditures.But even putting aside those concerns, I think the paper's conclusions are telling in regard to the Forks vs. Feet debate.Clearly both forks and feet are thermodynamically implicated in obesity.In one corner, taking this paper to be true (true despite the fact doubly labeled water studies that actually measure total daily energy expenditures suggest otherwise), we've now got 100 calories a day we're not burning due to less physically demanding jobs. In the other corner we've got energy intake data reporting adults are consuming 500 more calories daily now as compared with 1970.Basically we're looking at a 600 calorie surplus. 100 from fitness and 500 from food. Put another way, our modern caloric excess is 83% food and 17% fitness, not exactly a home run for the Feet camp, but damn close the 80/20 rule I tend to believe is true.Church, T., Thomas, D., Tudor-Locke, C., Katzmarzyk, P., Earnest, C., Rodarte, R., Martin, C., Blair, S., & Bouchard, C. (2011). Trends over 5 Decades in U.S. Occupation-Related Physical Activity and Their Associations with Obesity PLoS ONE, 6 (5) DOI: 10.1371/journal.pone.0019657Wilkin, T., Mallam, K., Metcalf, B., Jeffery, A., & Voss, L. (2006). Variation in physical activity lies with the child, not his environment: evidence for an ‘activitystat’ in young children (EarlyBird 16) International Journal of Obesity, 30 (7), 1050-1055 DOI: 10.1038/sj.ijo.0803331Luke, A., Dugas, L., Ebersole, K., Durazo-Arvizu, R., Cao, G., Schoeller, D., Adeyemo, A., Brieger, W., & Cooper, R. (2008). Energy expenditure does not predict weight change in either Nigerian or African American women American Journal of Clinical Nutrition, 89 (1), 169-176 DOI: 10.3945/ajcn.2008.26630Lara R Dugas, Regina Harders, Sarah Merrill, Kara Ebersole, David A Shoham, Elaine C Rush, Felix K Assah, Terrence Forrester, Ramon A Durazo-Arvizu, & Amy Luke (2011). Energy expenditure in adults living in developing compared with industrialized countries: a meta-analysis of doubly labeled water studies The American Journal of Clinical Nutrition, 93 (2), 427-441 : 10.3945/​ajcn.110.007278... Read more »

Church, T., Thomas, D., Tudor-Locke, C., Katzmarzyk, P., Earnest, C., Rodarte, R., Martin, C., Blair, S., & Bouchard, C. (2011) Trends over 5 Decades in U.S. Occupation-Related Physical Activity and Their Associations with Obesity. PLoS ONE, 6(5). DOI: 10.1371/journal.pone.0019657  

Luke, A., Dugas, L., Ebersole, K., Durazo-Arvizu, R., Cao, G., Schoeller, D., Adeyemo, A., Brieger, W., & Cooper, R. (2008) Energy expenditure does not predict weight change in either Nigerian or African American women. American Journal of Clinical Nutrition, 89(1), 169-176. DOI: 10.3945/ajcn.2008.26630  

Lara R Dugas, Regina Harders, Sarah Merrill, Kara Ebersole, David A Shoham, Elaine C Rush, Felix K Assah, Terrence Forrester, Ramon A Durazo-Arvizu, & Amy Luke. (2011) Energy expenditure in adults living in developing compared with industrialized countries: a meta-analysis of doubly labeled water studies. The American Journal of Clinical Nutrition, 93(2), 427-441. info:/10.3945/​ajcn.110.007278

  • May 30, 2011
  • 03:33 AM
  • 1,200 views

Mapping fitness: ribozymes, landscapes, and Seattle

by SFMatheson in Quintessence of Dust

A few months ago, we were looking at the concept of a fitness landscape and how new technologies are creating opportunities for biologists to look in detail at relationships between genetics and fitness. The first post discussed the concepts of a fitness landscapes and adaptive walks, with some focus on the limitations of the metaphor. The second post summarized some recent work on bacterial fitness and mutation rates, with the concept of a fitness landscape as a theme, and the third post reviewed another recent paper, one that described techniques for studying fitness landscapes in detail by linking protein function (which can be screened and/or selected) and genetic information. Here we'll look at yet another approach to the problem, in which the subject of the analysis is not an organism (as in the first paper) or a protein (as in the second paper) but an RNA molecule.

Recall that Fowler et al. set out to design a system in which one can study a protein's function (its “fitness”) as it varies in sequence. The idea is to look at all (or at least nearly all) of the variants of a particular protein to see how well each one works, and then to map this measure of fitness onto the sequence space of the protein. Such a map would be a form of fitness landscape. Fowler and colleagues (henceforth called the UW group) used a previously-known technique (protein display) to link each variant of the protein to its gene sequence, then used next-generation gene-sequencing technology to rapidly determine the gene sequences of millions of variants.

Last October, a group at the Fred Hutchinson Cancer Research Center in Seattle reported the results of a somewhat similar experimental effort. Jason Pitt and Adrian Ferré-D'Amaré co-authored the paper in Science, and their title identified their research objective: “Rapid Construction of Empirical RNA Fitness Landscapes.” The first couple of sentences of the abstract should sound familiar by now. (The genotype is the gene sequence. The phenotype is the function.)
Evolution is an adaptive walk through a hypothetical fitness landscape, which depicts the relationship between genotypes and the fitness of each corresponding phenotype. We constructed an empirical fitness landscape for a catalytic RNA by combining next-generation sequencing, computational analysis, and “serial depletion,” an in vitro selection protocol.And they identify two major challenges, both of which we have already discussed:
First, even for macromolecules of modest length, the sequence space is vast; a 20-mer RNA or protein has ~1012 or ~1026 possible sequences, respectively. Second, to characterize the landscape, the phenotypic fitness of each individual genotype needs to be measured, or an indirect measure of fitness needs to be validated.The authors tackled the challenges using a strategy very similar to that of the UW group: first they designed a functional screen, a way to subject an enormous population of variants to a gauntlet of selection, so that the population would be altered in structure after each round of selection. Think of it as evolution in a test tube. But the UW group had a problem that Pitt and Ferré-D'Amaré didn't have to worry about: the linkage of protein function with the underlying gene sequence. Why the difference? Pitt and Ferré-D'Amaré didn't study protein. They studied RNA – specifically, they analyzed the function of a ribozyme, which is a molecule of RNA that is capable of altering chemical reactions the way protein enzymes do. This means that there was no translation problem for them, since the gene sequence (the base sequence of the RNA) also comprises the structure of the molecule that is being functionally assessed.

So, like the UW group, they took a known molecule and made zillions of variants, through the use of random mutation. Then they assessed the function of the variants by putting them into pools (huge groups) and forcing them to compete with each other. (The competition involved binding to a specific target; the UW group used a similar approach.) Each round of competition (selection) led to the pool being enriched for “functional” molecules. And, importantly, they demonstrated that the binding competition really does select for function; that is, the selection process is enriching for higher “fitness.” After selection, they saw the enrichment that they expected: random sequences (added as a control) were depleted, whereas sequences very similar to the known “normal” sequence were enriched. And, interestingly, lots of other sequences were intermediate between those. Now, how can we graphically depict this? Pitt and Ferré-D'Amaré decided to plot the rate of change in frequency over time for each genotype (i.e., for each variant as identified by sequencing) against a representation of genotype space. The challenge of representing genotype space, or sequence space, is daunting: it will hardly do to put every sequence onto the axis of a graph. So the authors devised a similarity score as an indicator of sequence space, with the known normal sequence as the standard for comparison. And here is their empirical fitness landscape, from Figure 2B:


Each dot is a single sequence. (Actually, each dot is a whole set of sequences that have the same similarity to the reference sequence. In Figures 1C and 1E the authors introduce another dimension to show the spread that each dot represents.) The green dots show enrichment of sequences after 1 minute of competition; the reference sequence is on the far right, such that the steeply-sloping peak on the far right represents sequences that are similar to that reference sequence. As we might expect, the more similar a sequence is to the reference sequence, the more “fit” it is (in general). Fitness is indicated by extent of enrichment, which the authors term “fecundity.” The magenta dots represent not enrichment, but depletion; in a reciprocal experiment, the investigators removed the most fit molecules from the pool by subtracting the best-binding population from the pool. Notice that the depletion landscape is basically a mirror image of the enrichment landscape, as we would expect if the process is truly selecting based on binding activity.

There's a lot of data in that graph. Here's how the authors describe the result:
...the fecundity of any individual sequence provides a metric of its fitness, and we can create an experimental fitness landscape composed of ~107 different RNA genotypes in a single experiment.And yet the picture is a vast oversimplification of that huge data set. For one thing, the graph provides no specific sequence information even though the sequence of every one of those 10 million variants is known. Pitt and Ferré-D'Amaré write:
The empirical fitness landscape we generated is a high-dimensional object. We visualized it by computing the information content per residue of the master sequence, in essence projecting the landscape onto the ribozyme sequence.The resulting visualization (in Figure 4A) is a heat map of the actual structure of the catalytic RNA. It's simpler than it seems: each base in the RNA is colored according to information content as indicated on the color scale. More information means more diversity at that position; low information content means that there is little diversity at that position, indicating strong conservation due to functional constraint. The graph seems utterly unlike the topographical landscape that Sewall Wright sketched, but it's a fitness landscape nonetheless, made possible by the creativity of Pitt and Ferré-D'Amaré and by the power of next-generatio... Read more »

  • May 30, 2011
  • 02:32 AM
  • 1,343 views

Shamanic Initiations: A hidden Theme within the Fairy Tale of Hansel and Gretel

by Franco Bejarano in CulturePotion

While the fairy tale of "Hansel and Gretel" is often regarded as a coming of age story, the tale actually depicts another kind of rite of passage, that of shamanic initiations. The article is a comparative study with the narrative of initiation rituals around the world, along with other figures of folklore.
To say that by defeating the witch, one becomes a witch would be a paradox, especially in the genre of fairy tales that often demonizes witches, however, given the ambiguity attributed to folk tales, and their controversial pagan origins often suppressed by the Abrahamic religions, it is no surprise such elements are present. ... Read more »

Joan Halifax. (1990) The shaman's initiation. ReVision, 13(2), 53. info:/9607292149

  • May 30, 2011
  • 12:04 AM
  • 1,428 views

The Rise of Animals

by Marc in Teaching Biology

Part 2 of a 6-talk series on the history of life on Earth I held in Cyprus.

At the end of the Proterozoic, from ~700 to 535.1 million years ago, a unique ecosystem developed inhabited by what is known as the Ediacaran Biota. The affinities of most of these organisms (if they are even organisms!) will always be disputed, but it is relatively sure that among sponges and jellyfish, the direct ancestors of the animal phyla we know today were lurking among them.

The start of the next period, the Cambrian, is dominated by what is known as the Cambrian Radiation, an event in which ecology and animal life as we know it arose in a period of 20-30 million years. The animal phyla of today – chordates, arthropods, echinoderms, etc. – originated in this sudden burst of evolution.

An extinction event at the end of the Cambrian was followed by various radiations and smaller extinctions, during which most of the major orders of animal life originated.

This talk will go from cover 300 million years, from ~700 Ma to ~400 Ma, to review these events. It will be informed by the spectacular fossil localities available from these times, which preserve the unique animals in exquisite detail.... Read more »

  • May 29, 2011
  • 10:53 PM
  • 991 views

Health effects from chemical exposures – not just a modern phenomenon

by Ashartus in exposure/effect

When we think about exposures to chemicals causing adverse effects on human health, there is a tendency to view this as a product of modern industrial societies. To some extent this is true – there are certainly potentially hazardous chemicals we are exposed to as a result of our lifestyles, such as volatile chemicals in [...]... Read more »

  • May 29, 2011
  • 06:20 PM
  • 1,581 views

How chilled are the religious and non-religious?

by Tom Rees in Epiphenom

When you get in a stressful situation, your heart rate goes up and your blood pressure rises - the classic 'fight or flight' response. Not all people react the same, however.

Kevin Masters, of the University of Colorado, and Andrea Knestel (Brigham Young University), decided to test whether religious and non-religious people react differently to stress. People who do react badly to stress are more likely to die young, and they were wondering if this might help explain the differences in life expectancy between the religious and non-religious.

So they advertised for people to come into their lab (they got 131 people in total, aged between 40-70 years). Then they stressed them!

The stress task involved a spot of mental arithmetic, followed by role-playing (having a row with a medical insurance rep over a claim - a typically American situation!). They first had to spend 5 minutes preparing (aka fretting), and the role-play was filmed - just to add to the stress.

A third of their group was non-religious, and they divided their religious subjects according to whether they were intrinsically religious (i.e. for their own, internal reasons), extrinsically religious (because they love all the external trappings - the social activities, social status etc). Religious people who were both intrinsically and extrinsically religious were called 'pro-religious'.

Well, it turned out that too few religious people would admit to being solely motivated by extrinsic motives. So they only got the 'pro-religious', and an equal number of intrinsically religious.

Well, the strange thing was that the non-religious and the intrinsically religious reacted similarly badly to stress, while the pro-religious were better than either of the other two groups.

It's a bit of a mystery why this should be - the researchers admit that it's not what they were expecting. The pro-religious group also said that they thought the situation, if they experienced it for real, would not be that stressful.

Interestingly, although (like everyone) the pro-religious initially volunteered for the experiment, they were the hardest to track down and follow up on. That's pretty characteristic of extrinsically motivated people in general - they work hard at creating an appearance of being committed and hard-working, but are less interested in following through. Perhaps they were just less empathic.

The pro-religious were also more neurotic. Neurotic people have previously been shown to react with less stress in this sorts of task.

But I think there is something else going on here. Studies of the relationship between religion and health have found that it's not the believing that matters, but the attending. People who go to Church more often are healthier.

Going to Church (mixing with other people, using religion as a tool to improve your social status) is exactly what distinguishes the 'pro-religious' from the intrinsically religious and the non-religious. Could it simply be that the 'pro-religious' are more confident in themselves, as a result of being embedded in society, and so find it easier to brush stress off?

And might this help explain why church-goers tend to live a little longer?


Masters KS, & Knestel A (2011). Religious motivation and cardiovascular reactivity among middle aged adults: is being pro-religious really that good for you? Journal of Behavioral Medicine PMID: 21604184

This article by Tom Rees was first published on Epiphenom. It is licensed under Creative Commons.



... Read more »

  • May 29, 2011
  • 05:47 PM
  • 1,320 views

Racing male tree bumblebees

by Africa Gomez in BugBlog

In the last two weeks, the garden has been overtaken by frenzied male bumblebees. They follow a set circuit around the garden, round and round, racing from bush to bush and then having a little bumble in each. If you wait a bit on a particular spot on the route, you are likely to see another bumblebee a few minutes later passing by in the same direction, doing exactly the same. Most of the males I have been able to identify doing this are Bombus hypnorum. Today, a male B. hypnorum - which can be distinguished from the female by his white moustache - got trapped inside the conservatory and I had his portrait taken (above). Many male bumblebees have recently emerged from their nests, never to return, and their mission is to find queens and mate with as many as possible. In many bumblebee species, males' strategy consists on marking a route, sometimes hundreds of meters long, often circular, depending on the species, and marking certain places along the route with pheromones produced by scent glands in their jaws. Males join already set routes and therefore many males, some of them probably their siblings, go round the same routes every day, stopping to feed occasionally. Queens encountering a route are attracted by the pheromone and are then intercepted by males. The discovery and first description of these male bumblebee flight paths - from Bombus hortorum males - dates back to Charles Darwin, from observations he carried out at Down House. Although he didn't realise pheromones were involved, he noticed bumblebee routes and them stopping and bumbling at places he called "buzzing places", and marveled at the fact that the same or very similar routes were used year after year:I then followed their route for about a hundred and fifty yards until they came to a tall ash, and all along this line they buzzed at various fixed spots. At the far end, near a pollard oak, the track divided into two as shown in the plan. On some days all the bees flew in the direction I have described, but on others some arrived from the opposite direction. From observations made on favourable days, I think that the majority of individuals must fly in a wide circle. They stop every now and then to suck at flowers. I confirmed that whilst in flight they move at about ten miles an hour, but they lose a considerable amount of time at the buzzing places. The routes remain the same for a considerable time, and the buzzing places are fixed within an inch. I was able to prove this by stationing five or six of my children each close to a buzzing place, and telling the one farthest away to shout out " here is a bee " as soon as one was buzzing around. The others followed this up, so that the same cry of " here is a bee " was passed on from child to child without interruption until the bees reached the buzzing place where I myself was standing.  This sketch of the grounds of Down House shows the part of the male bumblebee flight route studied by Darwin with the help of his children. What fun must have been to have him as a dad!ReferencesFreeman, R.B. (1968). Charles Darwin on the routes of male bumblebees. BULLETIN OF THE BRITISH MUSEUM (NATURAL HISTORY) HISTORICAL SERIES , 3 (6), 177-189.Stiles, Edmund W. (1976). Comparison of Male Bumblebee Flight Paths: temperate and tropical. Journal of the Kansas Entomological Society., 49 (2), 266-274.... Read more »

FREEMAN, R.B. (1968) Charles Darwin on the routes of male bumblebees. BULLETIN OF THE BRITISH MUSEUM (NATURAL HISTORY) HISTORICAL SERIES , 3(6), 177-189. info:/

  • May 29, 2011
  • 03:33 PM
  • 1,781 views

Gene Expression in Autistic Brain Tissue

by Lindsay in Autist's Corner

Discussion of a recent study finding differences in amount of mRNA corresponding to two gene networks in autistic vs. control brain tissue samples. My focus is primarily on what they did and how they did it --- I mention, but do not spend a whole lot of time on, what they found.... Read more »

Irina Voineagu, Xinchen Wang, Patrick Johnston, Jennifer K. Lowe, Yuan Tian, Steve Horvath, Jonathan Mill, Rita M. Cantor, Benjamin J. Blencowe, & Daniel H. Geschwind. (2011) Transcriptomic analysis of autistic brain reveals convergent molecular pathology. Nature. info:/10.1038/nature10110

  • May 29, 2011
  • 02:05 PM
  • 1,310 views

Beneficial Biological Effects of Polyhydroxy Fullerenes

by Michael Long in Phased

A nanomaterial commonly presumed to be universally toxic appears to be beneficial to algae, plants, fungi, and invertebrates.... Read more »

  • May 29, 2011
  • 09:30 AM
  • 1,562 views

Cambodia: now with dibamids!

by Darren Naish in Tetrapod Zoology





Dibamids are a weird and very neat group of fossorial, near-limbless squamates that I've long planned to cover at Tet Zoo. Little is known about them and how they might relate to other squamates has long been the subject of debate (they might be close to amphisbaenians, but links with gekkotans, skinks and snakes have all been suggested in the past). I'm going to avoid saying much about them here: I just want to point to the fact that a newly named species - Dibamus dalaiensis Neang et al., 2011 [shown here; image Thy Neang/Flora & Fauna International] - extends their distribution to Cambodia. The previously recognised species of Dibamus are known from south-east Asia, India, southern China, New Guinea and the Philippines, but another dibamid - Anelytropsis papillosus (first described by Cope in 1885) - is endemic to Mexico. Read the rest of this post... | Read the comments on this post...... Read more »

Townsend TM, Leavitt DH, & Reeder TW. (2011) Intercontinental dispersal by a microendemic burrowing reptile (Dibamidae). Proceedings. Biological sciences / The Royal Society. PMID: 21270029  

  • May 29, 2011
  • 06:04 AM
  • 1,162 views

Do Antidepressants Work? The Internet Says...

by Neuroskeptic in Neuroskeptic

..."yes and no". A while back I blogged about some researchers who analysed internet discussions of antidepressants to work out what users thought about them. Now a new paper's just come out, doing much the same thing but focussed on a single comment thread: Miracle Drug, Poison, or Placebo.Back in 2008, MSNBC ran this article, prompted by the recent publication of the famous Kirsch paper. The article itself was short but the ensuing discussion in the comments rapidly grew to epic proportions. By the end of it there were a total of 1,629 posts by a total of over 1,200 people.In the new paper, author Michael Montagne presents an analysis of the thread. He read through all of the postings and focussed on the ones written by people who had personally taken antidepressants. After excluding obvious spammers and other undesirables (see the picture...), there were still 960 antidepressant users who wrote 1,231 posts.He first looked to see how many people thought antidepressants were "miracle drugs, poisons, or placebos", which was the title of the original article. However, only a handful of people used those terms in their comments. Almost everyone agreed that antidepressants were not just placebos.Users employed a range of metaphors to describe the experience. 45 people described them as "livesaving" and 8 said they were a "Godsend". But 21 accused them of turning them into "a zombie".Down at the bottom of the list were some more unique phrases that only one person used such as "Unleashes a 100 blind monkeys in your brain with instructions to rewire", "Uberpositive girl" and "Robot-zombie wrapped in 4 inches of insulation". That last one could be quite a good horror movie actually.While there were a small number of absolutely negative comments like "evil" and "Devil's drug", the most consistent theme in the metaphors was that of emotional numbing, with the idea that these drugs remove the symptoms by removing the ability to feel (see e.g. "zombie", "robot", "disconnected", "in a bubble", "band aid".) which seems rather ambivalent. However, only about 10% of the users used any metaphors at all, so take that with a pinch of salt.Even more salt is required for this graph I made from the table showing the number of positive, negative and mixed judgements on each antidepressant. I've not shown the data from drugs like tricyclics where there were less than 20 total responses. It's interesting, though, that people tended to be more positive about specific drugs than they were when talking about "antidepressants" in general.There were various other themes in the comments including an ongoing debate between people who said that depressed people ought to seek help from God (who tended to be non-users) vs those who disagreed (who tended to be users). Overall it's an interesting read, but I think it's one of those papers that's more interesting than it really deserves to be. At the end of the day, it's one comment thread on one article on one site.Montagne M (2011). Miracle drug, poison, or placebo: patients' experiences with antidepressant medications as described in postings on an online message board. Substance use & misuse, 46 (7), 922-30 PMID: 21599508... Read more »

  • May 29, 2011
  • 01:47 AM
  • 1,903 views

Yet Another Call to Arms

by Paige Brown in From The Lab Bench

A recent Salmonella outbreak hit 35 states, causing 73 infections and 1 death according to the Centers for Disease Control and Prevention (CDC), reporting on incidents this April.The recent outbreak is cause for special concern, because it was discovered to have originated in clinical and teaching microbiology laboratories, controlled environments where appropriate safety regulations are supposedly enforced. ... Read more »

Hayden EC. (2011) Salmonella hits US teaching labs. Nature, 473(7346), 132. PMID: 21562531  

  • May 28, 2011
  • 07:59 PM
  • 1,177 views

Barriers to recovery. What stops people going to AA and NA?

by PeaPod in Binge Inking

For people with alcohol and other drug problems, going to mutual aid groups like Alcoholics Anonymous and Narcotics Anonymous is associated with a variety of benefits. Barriers can be created preventing helpful engagement. This paper explored these. The findings are surprising.... Read more »

  • May 28, 2011
  • 06:45 PM
  • 1,229 views

Are we ‘illiterate listeners’? [Part 2]

by Henkjan Honing in Music Matters

This week a fragment from The Illiterate Listener that will be published later this year at Amsterdam University Press:"French babies cry differently than German babies. That was the conclusion of a study published at the end of 2009 in the scientific journal Current Biology. German babies were found to cry with a descending pitch; French babies, on the other hand, with an ascending pitch, descending slightly only at the end. It was a surprising observation, particularly in light of the currently accepted theory that when one cries, the pitch contour will always descend, as a physiological consequence of the rapidly decreasing pressure during the production of sound. Apparently, babies only a few days old can influence not only the dynamics, but also the pitch contour of their crying. Why would they do this?The researchers interpreted it as the first steps in the development of language: in spoken French, the average intonation contour is ascending, while in German it is just the opposite. This, combined with the fact that human hearing is already functional during the last trimester of pregnancy, led the researchers to conclude that these babies absorbed the intonation patterns of the spoken language in their environment in the last months of pregnancy and consequently imitated it when they cried.This observation was also surprising because until now one generally assumed that infants only develop an awareness for their mother tongue between six and eighteen months, and imitate it in their babbling. Could this indeed be unique evidence, as the researchers emphasized, that language sensitivity is already present at a very early stage? Or are other interpretations possible?Although the facts are clear, this interpretation is a typical example of what one could call a language bias: the linguist’s understandable enthusiasm to interpret many of nature’s phenomena as linguistic. There is, however, much more to be said for the notion that these newborn babies exhibit an aptitude whose origins are found not in language but in music.We have known for some time that babies possess a keen perceptual sensitivity for the melodic, rhythmic and dynamic aspects of speech and music: aspects that linguists are inclined to categorize under the term ‘prosody’, but which are in fact the building blocks of music. Only much later in a child’s development does he make use of this ‘musical prosody’, for instance in delineating and subsequently recognizing word boundaries. But let me emphasize that these very early indications of musical aptitude are not in essence linguistic." Honing, H. (2011, in press). The illiterate listener. On music cognition, musicality and methodology. Amsterdam: Amsterdam University Press. ... Read more »

Honing, H. (2011) The illiterate Listener. On music cognition, musicality and methodology. Amsterdam University Press. info:other

  • May 28, 2011
  • 06:00 PM
  • 1,226 views

Bacteria for Low-Cost Alkaloid Production

by Michael Long in Phased

Widely-used medically-relevant compounds, often costly due to low-yield extraction from plants, are on their way to becoming readily and cheaply isolated from genetically engineered bacteria.... Read more »

Nakagawa, A., Minami, H., Kim, J.-S., Koyanagi, T., Katayama, T., Sato, F., & Kumagai, H. (2011) A bacterial platform for fermentative production of plant alkaloids. Nature Communications, 326. DOI: 10.1038/ncomms1327  

  • May 28, 2011
  • 03:18 PM
  • 1,490 views

Religious Evolution: Sami Sticks & Phoenician Stones

by Cris Campbell in Genealogy of Religion

Unlike living organisms, cultural formations do not “evolve.” Evolution, sensu stricto, is a biological process and not a cultural one. Despite this fact, some scholars have fruitfully deployed evolutionary ideas — as analogy and metaphor — to analyze cultural history.
In 1964 the sociologist Robert Bellah did just this in his classic paper, Religious Evolution. Taking [...]... Read more »

Bellah, R. (1964) Religious Evolution. American Sociological Review, 29(3), 358. DOI: 10.2307/2091480  

Stockton, Eugene D. (1974) Phoenician Cult Stones. Australian Journal of Biblical Archaeology, 1-27. info:/

  • May 28, 2011
  • 03:00 PM
  • 1,099 views

Tracking Stem Cells by MRI

by Sanford- Burnham in Beaker

How do we find out where stem cells go in the body. Dr. Evan Snyder and colleagues may have an answer.... Read more »

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