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  • September 13, 2011
  • 01:07 PM

Attack of the Warrior Gene Babies!

by nooffensebut in The Unsilenced Science

This is a look at the first study on the warrior gene’s effect on babies, and I reviewed the scientific literature on monoamine oxidase A (MAOA) in women and Asians, including epigenetics and gene expression, and hormone-gene interactions in aggression.... Read more »

Zhang M, Chen X, Way N, Yoshikawa H, Deng H, Ke X, Yu W, Chen P, He C, Chi X.... (2011) The association between infants' self-regulatory behavior and MAOA gene polymorphism. Developmental science, 14(5), 1059-1065. PMID: 21884321  

  • September 13, 2011
  • 11:30 AM

The importance of failure in graduate student training

by Southern Fried Scientist in Southern Fried Science

Running the winch at dusk The A-frame shuddered as the box core, heavy with mud and reeking of sulfur, emerged from the water. We knew that it had found its mark 2300 meters below. Soft sediment from the seafloor oozed out the sides as I slid the safety pins into the spade arm. [...]... Read more »

  • September 12, 2011
  • 12:14 PM

Going bananas over RotPotA...

by Kausik Datta in In Scientio Veritas

Caveat Lector: This post may contain what one might consider spoilers. Therefore, if you haven't already watched the 2011 movie "Rise of the Planet of the Apes" and are planning to do so, please cease and desist from reading...... Read more »

  • September 11, 2011
  • 01:49 PM

Neuroscience Fails Stats 101?

by Neuroskeptic in Neuroskeptic

According to a new paper, a full half of neuroscience papers that try to do a (very simple) statistical comparison are getting it wrong: Erroneous analyses of interactions in neuroscience: a problem of significance.Here's the problem. Suppose you want to know whether a certain 'treatment' has an affect on a certain variable. The treatment could be a drug, an environmental change, a genetic variant, whatever. The target population could be animals, humans, brain cells, or anything else.So you give the treatment to some targets and give a control treatment to others. You measure the outcome variable. You use a t-test of significance to see whether the effect is large enough that it wouldn't have happened by chance. You find that it was significant.That's fine. Then you try a different treatment, and it doesn't cause a significant effect against the control. Does that mean the first treatment was more powerful than the second?No. It just doesn't. The only way to find that out would be to compare the two treatments directly - and that would be very easy to do, because you have all the data to hand. If you just compare the two treatments to control you might end up with this scenario:Both treatments are very similar but one (B) is slightly better so it's significantly different from control, while A isn't. But they're basically the same. It's probably just fluke that B did slightly better than A. If you compared A and B directly you'd find they were not significantly different.An analogy: Passing a significance test is like winning a prize. You can only do it if you're much better than the average. But that doesn't mean you're much better than everyone who didn't win the prize, because some of them will have almost been good enough.Usain Bolt is the fastest man in the world (when he's not false-starting himself out of races). Much faster than me. But he's not much faster than the second fastest man in the world.Nieuwenhuis S, Forstmann BU, & Wagenmakers EJ (2011). Erroneous analyses of interactions in neuroscience: a problem of significance. Nature neuroscience, 14 (9), 1105-7 PMID: 21878926... Read more »

  • September 11, 2011
  • 11:12 AM

How much 9/11 TV footage is too much?

by Stuart Farrimond in Dr Stu's Science Blog

Ten years on from the fateful and tragic day, once again our TV screens relive the moments when the World Trade Centre and the Pentagon came under terrorist attack. Footage of planes exploding into skyscrapers, crumbling buildings and billowing dust clouds are all now indelibly etched into all of our psyches. It was a watershed … Continue reading »... Read more »

  • September 10, 2011
  • 08:22 AM

Agriculture and biodiversity conservation: to spare or to share, that is the question

by M. Balzan in Bioblog: the biodiversity blog

Small scale agriculture within the central Mediterranean island of Gozo (Malta): "in the Mediterranean region ... rich biodiversity has existed for millenia in an agricultural setting" (Godfray 2011)A report relating agricultural practices to biodiversity conservation in tropical environments has been published in the journal Science last week. Within this contribution, the researchers from the University of Cambridge, related the diversity of birds and trees within several landscapes in Ghana and India to the estimated yield for the area. With a world population projected to grow to 9 billion within the next 50 years, feeding the world, and especially meat-rich diets (until now) characteristic of the Western world, is likely to become an increasingly challenging task and more likely to influence the sustainability of our planet. Prof. Charles J. Godfray from the University of Oxford explains in the same journal, that in the face of these threats conservationists have for long debated how to best preserve biodiversity. Two theoretically contrasting strategies which have received substantial attention from conservationists are “land sharing” and “sparing”. Land sharing involves the simultaneous use of agricultural landscapes for less intense cultivation and biodiversity conservation. Contrastingly, land sparing aims at maximising agricultural produce from some land in order to allow other land to be set aside for conservation. Within the study conducted in Ghana and India the populations of birds and trees within several 1km2 landscapes were surveyed. These landscapes consist of a mosaic of habitats, ranging from natural forests to farmland. And for each of these the authors calculated the total agricultural yield and related this to the population size of each of these bird and tree species. The results suggest that most of the species were negatively affected by agriculture than benefited from it. This leads the authors to advocate land sparing as the most effective land-use strategy for ensuring biodiversity conservation and to propose alternative management strategies for protected areas in order to ensure natural habitat protection. This study raises several important questions with respect to current sustainable agriculture strategies adopted world-wide with the aim of sustaining biodiversity in rural landscapes. However, as the authors stress, it only offers a simple contrast between sharing and sparing ignores many of the complexities of biodiversity conservation and sustainable agriculture. Indeed, within the past years conservationists and researches have employed much energy in developing wildlife-friendly practices in agricultural landscapes which may enhance conservation therein. In the current realities of a growing human population, and a wealthier one, our agricultural practices must move away from current strategies, and we are indeed at cross-roads. Sustaining agricultural yield (and thus food security) for the world population will require either new methods and technologies, or a larger land use dedicated to agriculture. And a quick look at what’s on the plate right now for global agriculture suggests two emerging realities, which although not necessarily always congruent with “land sharing” and “sparing” can be thought of as being in line with these concepts. agricultural intensification: increased land use dedicated to monocultures; increased external inputs, use of broad spectrum chemicals; GM crops ecological intensification: organic farming, agri-environmental schemes (AES), ecosystem services In the last decades, probably also brought about by an increased public awareness of health effects of pesticides, organic farming has picked up as a more ecological alternative to conventional agriculture. Within the EU agri-environmental schemes are designed, at least in part, to enhance levels of biodiversity in farmland (Whittingham 2011) and organic farming is encouraged under AESs. The positive effects of organic farming on biodiversity within farmland is well documented, and species colonisation of agricultural land has been shown to increase with time since transition to organic farming (Jonason et al. 2011)⁠, which is an important result that contrasts the idea of separating conservation from agriculture.... Read more »

  • September 8, 2011
  • 10:28 AM

FUTON Bias. Or Why Limiting to Free Full Text Might not Always be a Good Idea.

by Laika in Laika's Medliblog

A few weeks ago I was discussing possible relevant papers for the Twitter Journal Club  (Hashtag #TwitJC), a succesful initiative on Twitter, that I have discussed previously here and here [7,8]. I proposed an article, that appeared behind a paywall. Annemarie Cunningham (@amcunningham) immediately ran the idea down, stressing that open-access (OA) is a pre-requisite for the TwitJC [...]... Read more »

Björk, B., Welling, P., Laakso, M., Majlender, P., Hedlund, T., & Guðnason, G. (2010) Open Access to the Scientific Journal Literature: Situation 2009. PLoS ONE, 5(6). DOI: 10.1371/journal.pone.0011273  

Matsubayashi, M., Kurata, K., Sakai, Y., Morioka, T., Kato, S., Mine, S., & Ueda, S. (2009) Status of open access in the biomedical field in 2005. Journal of the Medical Library Association : JMLA, 97(1), 4-11. DOI: 10.3163/1536-5050.97.1.002  

WENTZ, R. (2002) Visibility of research: FUTON bias. The Lancet, 360(9341), 1256-1256. DOI: 10.1016/S0140-6736(02)11264-5  

Murali NS, Murali HR, Auethavekiat P, Erwin PJ, Mandrekar JN, Manek NJ, & Ghosh AK. (2004) Impact of FUTON and NAA bias on visibility of research. Mayo Clinic proceedings. Mayo Clinic, 79(8), 1001-6. PMID: 15301326  

Carney PA, Poor DA, Schifferdecker KE, Gephart DS, Brooks WB, & Nierenberg DW. (2004) Computer use among community-based primary care physician preceptors. Academic medicine : journal of the Association of American Medical Colleges, 79(6), 580-90. PMID: 15165980  

  • September 7, 2011
  • 07:43 AM

Behind the Headlines: ‘9/11 Counselling Drives People Mad’ – Is this Tabloid Journalism at its Worst?

by Stuart Farrimond in Dr Stu's Science Blog

Where were you when the Twin Towers came down? Most of us can remember. The terrorist attacks of September 11 stirred nations to war; triggered a decade of ‘Islamophobia’– and some even say – unified the people of USA. It has been the most televised and reported event in modern history. In the hours and … Continue reading »... Read more »

  • September 7, 2011
  • 01:48 AM

Tips when starting Psychiatry

by Dr Shock in Dr Shock MD PhD

Buffer During clerkship or residency individuals new to psychiatry find it hard to accommodate. Psychiatry rotation is still not compelled for GP’s and emergency medicine while these are probably the first to encounter psychiatric patients in different forms of distress. For those starting a rotation of psychiatry being it clerkship or otherwise here are a [...]

No related posts.... Read more »

Burkes, M., Hanna, L., & Woollard, J. (2011) Tips for GP trainees working in psychiatry. British Journal of General Practice, 61(583), 148-149. DOI: 10.3399/bjgp11X556407  

  • August 31, 2011
  • 01:34 AM

Advice to become a refined self-plagiarist. (Disclaimer: it is not ethical and will not help your career)

by Pablo Artal in Optics confidential

Some comments on self-plagiarism practices in science that will damage your career... sooner than later... Read more »

  • August 30, 2011
  • 02:13 AM

Social Media and Surgery

by Dr Shock in Dr Shock MD PhD

Buffer Surgeons not being the most social animals among doctors, I was surprised to see 7 editorials about surgery and social media. These seven editorials highlighted the use of social media and different settings for surgeons, from medical school all the way up to the American College of Surgeons. The most factual contribution was about [...]

No related posts.... Read more »

  • August 26, 2011
  • 02:49 PM

Part 2 of 2: Inflammation and Exercise: friend or foe?

by Kausik Datta in In Scientio Veritas

As I mentioned in Part 1 of this two-part post, inflammation is a two-edged sword, requiring a fine balance between initiation and termination, in order to promote health and not disease. With this idea in mind, I came across...... Read more »

Grounds MD, White JD, Rosenthal N, & Bogoyevitch MA. (2002) The role of stem cells in skeletal and cardiac muscle repair. The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society, 50(5), 589-610. PMID: 11967271  

Krause MP, Liu Y, Vu V, Chan L, Xu A, Riddell MC, Sweeney G, & Hawke TJ. (2008) Adiponectin is expressed by skeletal muscle fibers and influences muscle phenotype and function. American journal of physiology. Cell physiology, 295(1). PMID: 18463233  

Suzuki K, Nakaji S, Yamada M, Liu Q, Kurakake S, Okamura N, Kumae T, Umeda T, & Sugawara K. (2003) Impact of a competitive marathon race on systemic cytokine and neutrophil responses. Medicine and science in sports and exercise, 35(2), 348-55. PMID: 12569227  

  • August 26, 2011
  • 02:44 PM

Part 1 of 2: Inflammation: A two edged sword

by Kausik Datta in In Scientio Veritas

Inflammatory mechanisms are very important for the innate defence system of the body. When the host body encounters stimuli it perceives as harmful, such as pathogens and/or products thereof, injured cells or tissue, or any foreign object that irritates...... Read more »

Casadevall, A., & Pirofski, L. (2003) The damage-response framework of microbial pathogenesis. Nature Reviews Microbiology, 1(1), 17-24. DOI: 10.1038/nrmicro732  

  • August 26, 2011
  • 02:50 AM

Does internationalization change research content?

by Ingrid Piller in Language on the Move

Every linguistics undergraduate student is by now familiar with the fact of linguistic imperialism in academic publishing where the pressure to publish in international journals translates into the pressure to publish in English, leaving researchers from non-English-speaking backgrounds at a … Continue reading →... Read more »

  • August 26, 2011
  • 01:42 AM

A Whole New World: My Beginnings as a Student of Journalism

by Paige Brown in From The Lab Bench

This week, I started graduate classes for the first time as a student of Mass Communications at the LSU Manship School. Yahoo!
Thus begins my jump from a PhD in Biomedical Engineering to an advanced degree studying science journalism!
... Read more »

PH Longstaff. (2005) Security, resilience, and communication in unpredictable environments such as terrorism, natural disasters, and complex technology. Center for Information Policy Research. info:/

  • August 24, 2011
  • 08:00 AM

Taxonomy in decline or growth?

by Zen Faulkes in NeuroDojo

Earlier this year, Craig McClain from Deep Sea News wrote an editorial at Wired arguing that taxonomy as a scientific discipline was “going extinct.”

A short new paper challenges that view.

Joppa and colleagues looked at taxonomic research on cone snails (pictured), spiders, amphibians, birds, reptiles, and mammals. The number of taxonomists studying each group has gone up in every case, not down.

The number of species being described is also going up, but it is actually not keeping up with the growth of taxnomists: the average number of new species described by each taxonomist is getting smaller. It’s also noteworthy that taxonomists are not working alone, contrary to popular conceptions of expertise for whole groups being locked in the head of single individuals.

Can the perception of taxonomy as a discipline in decline be reconciled with the data? First, the data only goes to 2000. A lot has changed in ten years, though I don’t know if it has changed that much. Second, the authors suggest that taxonomy in North America and Europe might be running counter to a global trend: declining here while growing in the rest of the world.

Another idea I have that might explain the discrepancy is that there is no control group. The number of taxonomists may be increasing, but how does it compare to other disciplines in biology? I suspect that there has been healthy growth of biological sciences as a whole, and that while the number of taxonomists may have increased “exponentially” (as described by Joppa and colleagues), other fields, like cell and molecular biology, have increased even more exponentially. (Mathematicians, don’t bug me if that is a meaningless phrase.)


Joppa L, Roberts D, & Pimm S (2011). The population ecology and social behaviour of taxonomists Trends in Ecology & Evolution DOI: 10.1016/j.tree.2011.07.010

Photo by richard ling on Flickr; used under Creative Commons license.... Read more »

  • August 23, 2011
  • 10:43 PM

Microfluidics Education

by Hector Munoz in Microfluidic Future

The extent to which someone develops their passion and calling for is affected by when they are exposed to it, if it all. It wasn't until 2009 (the summer before my junior year) that I was first exposed to microfluidics when Dr. John T McDevitt came to Rice University. I wish I had met him earlier, because I was hooked from then on, and knew that I wanted to enter the field. Although I had been somewhat familiar with nanotechnology and MEMS since high school, I had never heard anything about microfluidics. I can only imagine what would have happened if I had started learning about the field when I was in high school. With the increasing presence of the microfluidics, it only makes sense to have people learn about it before they're working on it for their Master's or PhD, or seeing it in the news. That's the goal of Dr. Michelle Khine et al. of University of California Irvine. In case you're not familiar with Dr. Khine, you may remember her as one of the 2009 TR35 recipients. It's an award by MIT's Technology Review that recognizes young innovators under 35.In the paper "Shrink-film microfluidic education modules: Complete devices within minutes," which was published in Biomicrofluidics in June 2011, they outline a plan to introduce the field to middle schools, high schools and undergraduate programs. When compared to standard techniques, microfluidic systems can boast faster reaction times, portability and lower sample usage. Despite these advantages, they are still traditionally expensive to produce, which has limited their accessibility outside high-tech companies and universities. The authors of the paper note that thermoplastics (among other materials) are a low cost alternative fabrication technique that can also be used for education.Thermoplastics are essentially Shrinky Dinks you might have played with as a kid. You can draw on them, and they'll shrink when heated. The authors developed experiments using this material for middle school, high school and college classes, in which each level draws from and expands on the one before it. Using computer-aided design (CAD), the students are able to design their devices, and print them onto the plastic using a printer. After heating the plastic to shrink it to 95% its original size, it's used as a mold to create the device.H filterThe basic module for the middle school students is comprised of an H-filter. An H-filter is a simple microfluidic structure that is able to sort particles by their size without a membrane. The students replicate the filtration of blood using different sized microbeads. The results of the filtration can readily be seen.In addition to the previous module, high school students can build a microfluidic device that creates a gradient. A lot of biological processes are driven by gradients, making it a key environment to reproduce. The gradient generator design features branching and mixing channels that take inputs of plain water and dyed water to produce a gradient of concentrations at the end. Gradient GeneratorIn order to add a level of complexity for the gradient generator in a college classroom, it has been combined with an immunoassay. The channels of the structure are first coated with a primary antibody. A secondary fluorescent antibody is then fed through one inlet, as a serum is fed through the other. The resulting fluorescence indicates the same gradient occurs as was seen with the food dye previously.I think that this paper not only illustrates something cool to teach students, but takes it two steps further. It first illustrates some of the interesting characteristics of microfluidics such as diffusion mixing and laminar flow. It then illustrates possible applications of the technology in diagnostics or point-of-care devices. As microfluidics education grows, I think we'll eventually see grad students who started learning the same year as their mentors!Reference:Nguyen, D., McLane, J., Lew, V., Pegan, J., & Khine, M. (2011). Shrink-film microfluidic education modules: Complete devices within minutes Biomicrofluidics, 5 (2) DOI: 10.1063/1.3576930Claim token: blog4e48131515be7... Read more »

  • August 23, 2011
  • 11:54 AM

The Dubious Science of Teacher Coaching: "An Interaction-Based Approach to Enhancing Secondary School Instruction and Student Achievement"

by Chad Orzel in Uncertain Principles

A while back, I Links Dumped Josh Rosenau's Post Firing Bad Teachers Doesn't Create good Teachers, arguing that rather than just firing teachers who need some improvement, schools should look at, well, helping them improve. This produced a bunch of scoffing in a place I can't link to, basically taking the view that people are either good at what they do, or they're not, and if they're not, you just fire them and hire somebody else. I was too busy to respond at the time, but marked that doen as something to come back to. So I was psyched when I saw this paper in Science about a scientific trial of a teacher coaching service, which claims that:

The intervention produced substantial gains in measured student achievement in the year following its completion, equivalent to moving the average student from the 50th to the 59th percentile in achievement test scores.

"Ah-hah!" I said, "Scientific proof that teachers can, in fact, be improved with some extra instruction." So I sat down to go through the paper for ResearchBlogging purposes. Which is when I hit a problem, because the paper is kind of awful.

The awfulness isn't primarily on the scientific side, which is reasonably sound. They ran a controlled trial in Virigina with 78 teachers and more than 2000 students, randomly assigning teachers to the control and intervention groups. Teachers in the intervention group received coaching in making their classes more interactive, and regularly recorded themselves teaching then sent the recordings off for review. Experts at the coaching service being tested reviewed the recordings, then sent pointers to the teachers on what they could do better. They also followed up with a phone conversation.

The result wasn't all that dramatic, but in the year after the coaching, the teachers from the intervention group did substantially better than those from the control group. They measured performance by comparing student scores on the state-mandated end-of-year test the previous year to their performance on the state-mandated end-of-year test for the class being studied. The year after the trial, the intervention group's students improved from a raw score of 479 the previous year to a raw score of 488 for the year being studied, while the control group went from a raw score of 495 the previous year to 482 for the year being studied. This difference is statistically significant, and that's the origin of the 50th to 59th percentile claim.

So what's awful?

Read the rest of this post... | Read the comments on this post...... Read more »

  • August 22, 2011
  • 01:22 PM

Stoichiometric IR pulsed laser deposition of Yttrium doped Bi-2212 thin film

by nath in Imprints of Philippine Science

Yttrium-doped Bismuth Strontium Calcium Copper Oxide (BSCCO) films, specifically Bi 2212, were succesfully deposited with preserved sample concentration using Infrared Pulsed Laser Deposition (IR PLD) as written in a recent publication from the National Institute of Physics, University of the Philippines Diliman [1]. It was also shown that by using appropriate annealing, desired qualities for electronic applications can be obtained.... Read more »

  • August 21, 2011
  • 03:21 PM

PubMed’s Higher Sensitivity than OVID MEDLINE… & other Published Clichés.

by Laika in Laika's Medliblog

Is it just me, or are biomedical papers about searching for a systematic review often of low quality or just too damn obvious? I’m seldom excited about papers dealing with optimal search strategies or peculiarities of PubMed, even though it is my specialty. It is my impression, that many of the lower quality and/or less relevant papers are [...]... Read more »

Leclercq E, Kramer B, & Schats W. (2011) Limitations of the MEDLINE database in constructing meta-analyses. Annals of internal medicine, 154(5), 371. PMID: 21357916  

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