Post List

  • January 20, 2011
  • 05:30 AM

From bench to barn

by Becky in It Takes 30

Has synthetic biology ever gone further than this?  If so, I’m not aware of it.  A recent paper (Kemmer et al. 2010. A designer network coordinating bovine artificial insemination by ovulation-triggered release of implanted sperms. J. Controlled Release PMID: 21108977) starts by engineering a simple hormone-response circuit and ends with pregnant cows. First, a little [...]... Read more »

Kemmer C, Fluri DA, Witschi U, Passeraub A, Gutzwiller A, & Fussenegger M. (2010) A designer network coordinating bovine artificial insemination by ovulation-triggered release of implanted sperms. Journal of controlled release : official journal of the Controlled Release Society. PMID: 21108977  

  • January 20, 2011
  • 05:30 AM

What's in your kid's lunch bag?

by Yoni Freedhoff in Weighty Matters

Amazingly, despite the very basic fact that the food we provide our children is quite literally their bodies' building blocks, it would appear as if we're building our kids out of sugar and salt.Researchers over in the UK wanted to get a better look at packed lunches and so they undertook at cross-sectional survey that had 1,294 8-9 year old kids from 89 different British public schools work with researchers on a tool called the, "Lunch Box Evaluation Questionnaire".The results weren't heartwarming.Sandwiches were the most commonly packed foods and were most unfortunately followed by candy, savory snacks and sweetened drinks. The food least eaten? Fruit. Most eaten? Candy.Only 5.1% of packed lunches met what the study referred to as a "healthy standard" which consisted of, "a sandwich with protein filling (or alternative starchy and protein food), some vegetables, fruit, and a dairy product". 40% had both a confection and a savory snack (candies or cookies and chips). The average number of added teaspoons of sugar/lunch? 10.Those sure don't sound like ideal building blocks.Evans, C., Greenwood, D., Thomas, J., & Cade, J. (2010). A cross-sectional survey of children's packed lunches in the UK: food- and nutrient-based results Journal of Epidemiology & Community Health, 64 (11), 977-983 DOI: 10.1136/jech.2008.085977[Hat tip to my friend and colleague Sara Kirk]

... Read more »

  • January 20, 2011
  • 03:52 AM

Real-Time Visualization of DNA Transcription

by avi_wener in American Biotechnologist

Most of my graduate work focused on transcriptional regulation of a vasoregulatory gene and all the nitty-gritty work that goes along with these types of molecular protocols. As such, I am always on the lookout for techniques that improve upon current transcriptional regulation protocols especially if they show a propensity for doing the job either [...]... Read more »

L. Stirling Churchman, & Jonathan S. Weissman. (2011) Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature, 368-373. info:/doi:10.1038/nature09652

  • January 20, 2011
  • 03:49 AM

Retract That Seroxat?

by Neuroskeptic in Neuroskeptic

Should a dodgy paper on antidepressants be retracted? And what's scientific retraction for, anyway?Read all about it in a new article in the BMJ: Rules of Retraction. It's about the efforts of two academics, Jon Jureidini and Leemon McHenry. Their mission - so far unsuccesful - is to get this 2001 paper retracted: Efficacy of paroxetine in the treatment of adolescent major depression.Jureidini is a member of Healthy Skepticism, a fantastic Australian organization that Neuroskeptic readers have encountered before. They've got lots of detail on the ill-fated "Study 329", including internal drug company documents, here.So what's the story? Study 329 was a placebo-controlled trial of the SSRI paroxetine (Paxil, Seroxat) in 275 depressed adolescents. The paper concluded: that "Paroxetine is generally well tolerated and effective for major depression in adolescents." It was published in the Journal of the American Academy of Child and Adolescent Psychiatry (JAACAP).There's two issues here: whether paroxetine worked, and whether it was safe. On safety, the paper concluded that "Paroxetine was generally well tolerated...and most adverse effects were not serious." Technically true, but only because there were so many mild side effects.In fact, 11 patients on paroxetine reported serious adverse events, including suicidal ideation or behaviour, and 7 were hospitalized. Just 2 patients in the placebo group had such events. Yet we are reassured that "Of the 11, only headache (1 patient) was considered by the treating investigator to be related to paroxetine treatment."The drug company argue that it didn't become clear that paroxetine caused suicidal ideation in adolescents until after the paper was published. In 2002, British authorities reviewed the evidence and said that paroxetine should not be given in this age group.That's as maybe; the fact remains that in this paper there was a strongly raised risk. However, in fairness, all that data was there in the paper, for readers to draw their own conclusions from. The paper downplays it, but the numbers are there.*The efficacy question is where the allegations of dodgy practices are most convincing. The paper concludes that paroxetine worked, while imipramine, an older antidepressant, didn't.Jureidini and McHenry say that paroxetine only worked on a few of the outcomes - ways of measuring depression and how much the patients improved. On most of the outcomes, it didn't work, but the paper focusses on the ones where it did. According to the BMJStudy 329’s results showed that paroxetine was no more effective than the placebo according to measurements of eight outcomes specified by Martin Keller, professor of psychiatry at Brown University, when he first drew up the trial. Two of these were primary outcomes...the drug also showed no significant effect for the initial six secondary outcome measures. [it] only produced a positive result when four new secondary outcome measures, which were introduced following the initial data analysis, were used... Fifteen other new secondary outcome measures failed to throw up positive results. Here's the worst example. In the original protocol, two "primary" endpoints were specified: the change in the total Hamilton Scale (HAMD) score, and % of patients who 'responded', defined as either an improvement of more than 50% of their starting HAMD score or a final HAMD of 8 or below.On neither of these measures did paroxetine work better than placebo at the p=0.05 significance level. It did work if you defined 'responded' to mean only a final HAMD of 8 or below, but this was not how it was defined in the protocol. In fact, the Methods section of the paper follows the protocol faithfully. Yet in the Results section, the authors still say that:Of the depression-related variables, paroxetine separated statistically from placebo at endpoint among four of the parameters: response (i.e., primary outcome measure)...It may seem like a subtle point. But it's absolutely crucial. Paroxetine just did not work on either pre-defined primary outcome measure, and the paper says that it did.Finally, there were also issues of ghostwriting. I've never been that concerned by this in itself. If the science is bad, it's bad whoever wrote it. Still, it's hardly a good thing.*Does any of this matter? In one sense, no. Authorities have told doctors not to use paroxetine in adolescents with depression since 2002 (in the UK) and 2003 (in the USA). So retracting this paper wouldn't change much in the real world of treatment.But in another sense, the stakes are enormous. If this paper were retracted, it would set a precedent and send a message: this kind of p-value fishing to get positive results, is grounds for retraction.This would be huge, because this kind of fishing is sadly very common. Retracting this paper would be saying: selective outcome reporting is a form of misconduct. So this debate is really not about Seroxat, but about science.There are no Senates or Supreme Courts in science. However, journal editors are in a unique position to help change this. They're just about the only people (grant awarders being the others) who have the power to actually impose sanctions on scientists. They have no official power. But they have clout.Were the JAACAP to retract this paper, which they've so far said they have no plans to do, it would go some way to making these practices unacceptable. And I think no-one can seriously disagree that they should be unacceptable, and that science and medicine would be much better off if they were. Do we want more papers like this, or do we want fewer?So I think the question of whether to retract or not boils down to whether it's OK to punish some people "to make an e... Read more »

Keller MB, Ryan ND, Strober M, Klein RG, Kutcher SP, Birmaher B, Hagino OR, Koplewicz H, Carlson GA, Clarke GN.... (2001) Efficacy of paroxetine in the treatment of adolescent major depression: a randomized, controlled trial. Journal of the American Academy of Child and Adolescent Psychiatry, 40(7), 762-72. PMID: 11437014  

Newman, M. (2010) The rules of retraction. BMJ, 341(dec07 4). DOI: 10.1136/bmj.c6985  

  • January 20, 2011
  • 02:00 AM

Psychopaths chronic cheating and impulsive risky behaviors are linked to reasoning impairments

by SAGE Insight in SAGE Insight

Psychopaths are impaired in social exchange and precautionary reasoning   From Pychological Science Psychopaths persistently violate social, moral, and legal norms, cheating family, friends, and strangers alike. Two hallmarks of psychopathy are the persistent violation of social contracts and chronic, impulsive risky behavior. By testing incarcerated psychopaths this study considers if they understand what qualifies [...]... Read more »

  • January 20, 2011
  • 01:35 AM

Using board games to teach science

by helikonios in The view from Helicon

Elementary school students—even high school students—learn some fairly trite truisms about the scientific method that often aren’t clearly linked to the experimental results that are presented in textbooks as The Truth. A new paper in PLoS Biology makes a link between the codebreaking game Mastermind and teaching scientific reasoning skills to young students, in a [...]... Read more »

  • January 19, 2011
  • 10:55 PM

Elaborating Upon Titanium Dioxide Nanoparticle Pulmonary Toxicity

by Michael Long in Phased

Titanium dioxide nanoparticles interfere with intracellular calcium signaling and promote mucin protein secretion, directly implicating such nanoparticles in pulmonary toxicity (blocked airways).... Read more »

Chen, E. Y. T., Garnica, M., Wang, Y.-C., Chen, C.-S., & Chin, W.-C. (2011) Mucin Secretion Induced by Titanium Dioxide Nanoparticles. PLoS ONE, 6(1). DOI: 10.1371/journal.pone.0016198  

  • January 19, 2011
  • 09:51 PM

Book Review: When the Past is Always Present; A New PTSD Treatment?

by David Johnson, MSW, LICSW in Dare To Dream

by Ronald Ruden, MD, PhD
When the Past Is Always Present: Emotional Traumatization, Causes, and Cures introduces a new treatment for trauma. Ronald A. Ruden is an internal medicine physician practicing in Manhattan. Since beginning his practice in 1983, he has dedicated part of the proceeds to follow research interests. His first efforts resulted in the book, The Craving Brain, a neurobiological discussion of addictive behaviors. In 2003 he redirected his interest in understanding traumatization. That has led to three publications in Traumatology, edited by Charles Figley, and to this book.
Image via Wikipedia

The book begins with an easy to understand review of the neurobiological and neuropsychological literature as it relates to trauma. His intent is to provide a primer that a lay person could understand. He still provides adequate citations for those who have deeper interests.

Ruden believes that the means to treat Post Traumatic Stress Disorder (PTSD) is to use the senses. This idea, which is at the core of the theory of psychosensory therapy, forms what the author considers the "third pillar" of trauma treatment. The first and second pillars refer to psychotherapy and psychopharmacology. The theory of psychosensory therapy postulates that sensory input, for example, touch "creates extrasensory activity that alters brain function and the way we respond to stimuli". In other words, new sensory input can change memories and their power over us.

"...the human brain can change it's own structure and function with thought and experience, turning on its own genes to change its circuitry, reorganize itself and change its operation, is the most important alteration in our understanding of the brain in 400 years." (Norman Doidge, MD pXVII in Ruden, 2011)

This process of brain modification is called neuro-platisticity. Evidence of this concept has begun a revolution in thinking about the brain. No longer can one assume that brain damage creates an impermeable barrier to recovery. The point is we can change how well our brain functions if we work at it. If we neglect our brain, it will deteriorate before it's time. Yoga, mindfulness, meditation, and exercise enhance resilience. Resilience is associated with high self-esteem, good emotion regulation skills, optimism, healthy relationships, and an active problem solving response. When you believing you can meet your needs, you feel self-contained, like your world can be managed, you can respond to challenges and can readily find help if you need it. Vulnerability is increased by putting aside your needs to care for others, low self-esteem, difficulty in regulating the intensity and duration of emotions, obsessive-compulsive traits, introversion or being very shy, being anxiety prone, substance abuse, poverty and low education.

"In early life, when the limbic system has not completely formed (the hippocampus is not yet functional), highly emotional moments that occur become stored in a separate memory system called procedural [or implicit] memory.... The cognitive component of the event is not stored...." (Ruden, 2011, p24) When a child experiences trauma, the emotional memory is stored in a part of the brain not easily accessed by our thoughts, our conscious mind. But the memory is there ready to be triggered some event that reminds you of the traumatic memory. You may not even understand why you feel the intense emotions which will add to your confusion and anguish. Chronic release of stress chemicals by repeated triggered panic, changes the landscape of the brain producing self-defeating behavior and thinking, stress related disease, and vulnerability to further traumatization. Retraumatization may be related to repetition compulsion, a homeostatic driven need to heal. If you seek mastery over a situation without new skills to ensure success, the memory is triggered without the healing sense of safe haven, increasing the compulsion to seek mastery. Subconsciously, you may reenact the trauma by repeatedly exposing yourself to a similar trauma.

The second idea presented in this book is that traumatization is encoded into the implicit memory only under special circumstances. Traumatic memories are formed by an emotion-producing event with significant meaning to the individual, the brain must be appropriately primed to acute stress, and the event must be perceived as inescapable. (Ruden, 2011, p47) Encoding is completed at high norepinepherine and dopamine levels, while the prefrontal cortex is shut down. (Ruden, 2011, p59) Ruden insists the trauma must be perceived as inescapable for encoding as a traumatic memory. Feeling trapped, unable to escape takes the prefrontal cortex is taken off line, and we are unable to plan or think. (Ruden, 2011, p47-49) In my clinical experience, feeling trapped, responsible, and in some part to blame for the outcome also appears to play an important role in the development of PTSD.

"The third idea is that traumatization occurs because we cannot find a haven during the event. This is the cornerstone of havening, the particular form of psychosensory therapy described in the book. Using evolutionary biological principles and recently published neuroscientific studies, this book outlines in detail how havening touch de-links the emotional experience from a trauma, essentially making it just an ordinary memory. Once done, the event no longer causes distress." (Yaffe & Ruden Medical Associates)

Ruden's proposed treatment provides another method to unlearn these emotional reactions and retrieve a sense of mastery and safety after a traumatizing experience. Ruden's approach and other sensory-based techniques, are exposure based, a method that has extensive research support. Ruden's claims that animal research supports the notion that bilateral stimulation enhances healing is at best weakly supported by the studies cited.

Rasolkhani-Kalhorn & Harper (2006) appears to be Ruden's primary reference. The authors of this article acknowledge the limitations of the research support for their theory. They use anecdotal research evidence from animal studies to suggest that Eye-movement Desensitization and Reprocessing therapy (EMDR) and other psychosensory therapies, work by stimulating part of the brain to decouple the emotion from the memory. Those studies use fMRI, a scanning technique that can detect brain activity, and other methods. The idea is where there is brain activity when a person is doing something, identifies what parts of the brain are involved. However, every scan shows a lot of activity that is not understood and only some that is thought to be related. The method doesn't prove causation, only a relationship of co-occurance in time or correlation. There is no direct evidence that this correlation in animal brains will translate to human brains. There are real structural differences between humans and animals. So the research results at best only suggest that bilateral stimulation might be related to decoupling emotion from memories.

Ruden's theory is a bit different. When a traumatic event is recalled or reenacted while the survivor is in safe haven, the trauma-induced linkages are disrupted and the emotional response is subsides or is eliminated. According to Behavior Theory, a well research and widely accepted model, a conditioned emotional response is said to "extinguish" when it is repeatedly stimulated when the person feels safe. But Ruden's theory goes much fu... Read more »

Rasolkhani-Kalhorn, T., & Harper, M. (2006) EMDR and Low Frequency Stimulation of the Brain. Traumatology, 12(1), 9-24. DOI: 10.1177/153476560601200102  

Ruden, R. (2011) When the Past is Always Present. Psychosocial Stress Series. Routledge. info:other/978-0-415-87564-6

  • January 19, 2011
  • 09:34 PM

Keep Your International Arbitration out of the Tower of Babel

by Persuasion Strategies in Persuasive Litigator

By: Dr. Ken Broda-Bahm - So, a retired Brazilian judge, two American litigators, and three German engineers walk into a bar... Okay, so it wasn't a bar, it was an international arbitration, but the potential for miscommunication is just as great as the joke intro would imply. This one took place in Sao Paulo, Brazil and it was preceded by a two-day mock arbitration that I facilitated in order to help our litigation team prepare the best arbitration case possible. Any case that makes it to arbitration or trial faces its fair share of hurdles. The need to teach, to...... Read more »

  • January 19, 2011
  • 06:56 PM

Entomophagy: moths for dinner

by Chris Grinter in The Skeptical Moth

I have always known that in many places of the world, especially off the beaten track, caterpillars of moths and butterflies are on the menu.  From Africa to Australia there are dozens of species that might taste good enough to be reasonably edible or even delicious.  But here in the US insects rarely . . . → Read More: Entomophagy: moths for dinner... Read more »

  • January 19, 2011
  • 05:51 PM


by Sanford- Burnham in Beaker

Not all cells in a tumor are equal. They have different genes, proteins and behaviors and while some are easily killed, others are more resistant to cell-destroying therapies. In some cancers, a few of these hardier cells are cancer stem cells and they may be the culprits behind tumor formation and drug resistance. Much like [...]... Read more »

  • January 19, 2011
  • 05:20 PM

The Neuroscience of Fear and Loathing

by Shaheen Lakhan in Brain Blogger

Fear is an innate emotion that is triggered by environmental stimuli perceived as potentially threatening or harmful. This emotion is so basic to human existence that its expression on a human face can be accurately recognized by anyone in the world. Thus, fear is a highly evolved, universal emotion whose existence is critical to survival. [...]... Read more »

Ekman P, Sorenson ER, & Friesen WV. (1969) Pan-cultural elements in facial displays of emotion. Science (New York, N.Y.), 164(3875), 86-8. PMID: 5773719  

Feinstein JS, Adolphs R, Damasio A, & Tranel D. (2011) The human amygdala and the induction and experience of fear. Current biology : CB, 21(1), 34-8. PMID: 21167712  

Koenigs M, Huey ED, Raymont V, Cheon B, Solomon J, Wassermann EM, & Grafman J. (2008) Focal brain damage protects against post-traumatic stress disorder in combat veterans. Nature neuroscience, 11(2), 232-7. PMID: 18157125  

  • January 19, 2011
  • 05:00 PM

The Genetics of Pesticide Resistant Bedbugs

by Greg Laden in Greg Laden's Blog

Bedbugs (Insects of the Cimicidae family, commonly Cimex lectularius) are annoying, can carry diseases, and are apparently becoming more common in the US. Interestingly, there has been very little study done of their genetics. A new study just out in PLoS ONE looks at the bedbug genome in an effort to better understand pesticide resistance in these pesky critters.

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

Bai, X, & Et al. (2011) Transcriptomics of the Bed Bug (Cimex lectularius). PLoS ONE, 6(1). info:/

  • January 19, 2011
  • 05:00 PM

The Elephant's Chirp

by Shermin de Silva in Maximus

This is about one of those moments every scientist lives for: discovery. A new and mysterious elephant call, so soft and rare it barely registers conscious notice. To what end? No one knows.... Read more »

  • January 19, 2011
  • 04:24 PM

All about the attitude

by FrauTech in Design. Build. Play.

Does the old saying fake it old you make it hold any water? Turns out maybe. Researchers from Columbia and Harvard Universities posed subjects in one of four positions: two high power positions(expansive, open limbs) and two low power positions(contractive, closed limbs). Then they measured risk taking, self-response about feelings, and testosterone and cortisol.The high power positions were sitting stretched in a chair with legs propped up on a table and arms behind the head as well as leaning "confidently" over a table while standing. The low power positions were sitting in a chair with hands folded in the lap or standing with arms wrapped and legs crossed. I've helpfully recreated these in poorly drawn stick figures.A saliva sample was taken 10 minutes after the subject arrived as a baseline. And then later, 17 minutes after they had held their pose. They held each pose for 1 minute and were asked to focus on faces that were shown while holding the position. To measure risk taking they were given $2 and told they could either keep it or roll dice for a 50/50 chance of either losing it or doubling their money to $4. To get self-reported data they were asked how powerful and in charge they felt on a scale of 1 to 4.So what happened? The stress and testosterone showed correlation in that high power position resulted in higher testosterone and lower stress and the low power was the other way around. Of the high power posers 86% took the roll of dice versus 60% of the low power posers. The mean higher power self-rated "in charge" on a scale of 1 to 4 was 2.57 versus 1.83 for low power (both with a standard deviation of 0.81). So clearly there's something to this. But what exactly? With 42 participants I feel like the sample size is good enough to draw some conclusions. But it'd be nice to separate some of this out. Did taking a risk make them rank themselves as feeling more powerful? Is there any reason to believe the constricting positions were just less comfortable and possibly increased the stress hormone as a direct result? Still it seems to show the possibility that body posture can affect your own level of perceived confidence and a strong likelihood that it can cause slight fluctuations in your hormone levels. So maybe you can fake it until you make it.Carney, D., Cuddy, A., & Yap, A. (2010). Power Posing: Brief Nonverbal Displays Affect Neuroendocrine Levels and Risk Tolerance Psychological Science, 21 (10), 1363-1368 DOI: 10.1177/0956797610383437Want to see more of my writing? Check out Engineer Blogs where I and several other engineers blog about- well, what else, engineering.... Read more »

  • January 19, 2011
  • 02:11 PM

Should You Go With Your Gut?

by APS Daily Observations in Daily Observations

Have you ever relied on your gut feeling to make a decision? A new study published in Psychological Science suggests that while one’s “gut intuition” may be helpful when combined ... Read more »

Dunn, B.D., Galton, H.C., Morgan, R., Evans, D., Oliver, C., Meyer, M., Cusack, R., Lawrence, A.D., & Dalgleish, T. (2010) Listening to your heart: how interoception shapes emotion experience and intuitive decision making. Psychological Science, 21(12), 1835-44. PMID: 21106893  

  • January 19, 2011
  • 01:39 PM

Redefining the Kilogram

by Ryan K in A Quantum of Knowledge

There has been a movement in the physics world for that past few years to standardize the kilogram. At the moment, a kilogram is defined as the mass of the International Prototype Kilogram (IPK), housed at the International Bureau of Weights and Measures (BIPM). The prototype is made of 90% Platinum and 10% Iridium. The [...]... Read more »

Andreas, B., Azuma, Y., Bartl, G., Becker, P., Bettin, H., Borys, M., Busch, I., Gray, M., Fuchs, P., Fujii, K.... (2011) Determination of the Avogadro Constant by Counting the Atoms in a ^{28}Si Crystal. Physical Review Letters, 106(3). DOI: 10.1103/PhysRevLett.106.030801  

  • January 19, 2011
  • 01:00 PM

The Top 10 Medical TV Myths

by Stuart Farrimond in Dr Stu's Science Blog

Everyone loves a good hospital drama. They tick all the boxes for good TV: Gritty plots, life and death situations, steamy relationships, ethical dilemmas and blood and gore. Now more popular than ever, medical TV dramas have come a long way in the last 50 years. But just how accurate are they?

You might be surprised to discover just how many inaccuracies modern hospital TV dramas have in them. Here’s the Top 10 list of things you will only ever see in a TV hospital…... Read more »

Treakle AM, Thom KA, Furuno JP, Strauss SM, Harris AD, & Perencevich EN. (2009) Bacterial contamination of health care workers' white coats. American journal of infection control, 37(2), 101-5. PMID: 18834751  

  • January 19, 2011
  • 12:53 PM

Ringing in the New Year with Info Science Conferences: What social media do you use? #ALISE #HICSS

by Anatoliy Gruzd in Social Media Lab

Early January was a busy time for information science scholars, with two major conferences held in the United States.  Both the Association of Library and Information Science Educators (ALISE) Conference, and the Hawaii International Conference on System Sciences (HICSS) were held from January 4-7 this year.  Researchers from the Social Media Lab attended each to [...]... Read more »

Gruzd, A. . (2011) How Online Social Media and Networks Are Changing Scholarly Practice. Poster presented at the Association for Library and Information Science Education (ALISE) conference. info:/

  • January 19, 2011
  • 12:14 PM

Evidence Against The Universe Being Fine Tuned For Life.

by Joseph Smidt in The Eternal Universe

Many people will tell you that the universe appears fine tuned for life.  Don Page has decided to address this issue scientifically by calculating the best value for the cosmological constant needed to support life in the universe and then comparing it to our own.  His conclusion is that the cosmological constant is actually an example that our universe is not fine tuned for life.


... Read more »

Don N. Page. (2011) Evidence Against Fine Tuning for Life. E-Print. arXiv: 1101.2444v1

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