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  • April 9, 2011
  • 12:41 PM

The politics of the DSM 5 personality disorders

by Psychbytes in Psychbytes

Most science blog posts post a link to an academic article or two and discuss their merits or lack thereof. I am going to do something slightly different - I am linking to an entire special issue of a journal, with pdfs freely available online - and recommend that you do NOT waste any time reading any of it. All it really shows is a bunch of academics bickering over stuff that doesn't seem to make much of a difference. I imagine the DSM 5 PD workgroup meetings look something like this: South Korean politicians fighting Anyway, on to the articles. Out of all the changes being considered for the DSM 5, the personality disorder (PD) work group has proposed some of the most sweeping ones such as dropping 5 of the current PDs entirely and adding a dimensional component that somehow involved asssessing 6 trait domains and 37 facets  for the remaining PDs. Not surprisingly, this has not gone over too well.The Journal of Personality Disorders has recently published a special issue (see link here with pdfs) that has invited articles by the DSM PD workgroup members and other commentaries in response to it. I repeat - don't bother reading any of it. Most of these articles are filled with jargon (SNAP, DAPP, NEO, DIPSI, HEXACO, OMGWTFBBQ), are quite boring, appear to be selective in whatever literature they cite, with quite a few of the authors increasing their self-citation count, while sniping at each other. Here's a brief rundown.In the first article, the workgroup (Andrew Skodol et al.) rehash their proposal, but note that "Feedback from the [DSM-5] website posting suggested that this system was too complicated, redundant with the full clinicians’ trait ratings, and unwieldy". Really? Nah! Say it ain't so! So their solution is to separate the 5 PD "types", from the "traits" and "facets" in the field trials, and somehow refine this system. How? It is not entirely clear.In the next article (Krueger et al.), the authors repeatedly talk about the "empirical structure of personality". Curiously, while there is some overlap in authors with the first one, they are not all identical. I suspect this means some sort of division among the PD workgroup members. Anyway, as the authors themselves acknowledge, the bulk of the evidence for their proposal uses a statistical technique called factor analysis, which is essentially based on a whole lot of correlations. Why this makes the authors' proposal or review any more "empirical" is pretty unclear to me. The authors also take some effort to delineate why Thomas Widiger's (another big name in the personality world) preferred model of personality may not be as "empirical" as theirs.The remaining articles are commentaries. Clarkin and Huprich's, and Zimmerman's, are worth skimming over, but don't really say anything that wasn't already known - i.e., the PD proposal is too complex to be clinically useful, and not really based on much evidence. Then, we have an article by the aforementioned Widiger, who hits back pretty hard at Lee Anna Clark and Robert Krueger (two other big names) for not using his preferred model of personality, and spends 13 pages or so picking apart the PD proposal and Clark and Krueger's work.This is followed by a couple of articles by Robert Bornstein (an expert on Dependent PD) and Elsa Ronningstam (an expert on Narcissistic PD). These two PDs are slated to be dropped. So, no prizes for guessing what these commentaries are about. And lastly, Joel Paris has an article on the use of endophenotypes for diagnosing PDs - though as he clearly notes, we don't have any yet (which DSM disorder does anyway?). In other words, an academic exercise in what might be useful if we ever find it.While I occasionally use some personality inventories in my work, most of my work doesn't involve the PDs, and as such, I have no strong ties to a 5-, 6-, or 18-factor model of personality. I picked up this special issue hoping for some sort of enlightenment on the PD proposal. Now, instead, I wish I could get back the hours I spent reading these articles. Skodol AE, Bender DS, Morey LC, Clark LA, Oldham JM, Alarcon RD, Krueger RF, Verheul R, Bell CC, & Siever LJ (2011). Personality Disorder Types Proposed for DSM-5. Journal of personality disorders, 25 (2), 136-69 PMID: 21466247Krueger RF, Eaton NR, Clark LA, Watson D, Markon KE, Derringer J, Skodol A, & Livesley WJ (2011). Deriving an Empirical Structure of Personality Pathology for DSM-5. Journal of personality disorders, 25 (2), 170-91 PMID: 21466248Clarkin JF, & Huprich SK (2011). Do DSM-5 Personality Disorder Proposals Meet Criteria for Clinical Utility? Journal of personality disorders, 25 (2), 192-205 PMID: 21466249Zimmerman M (2011). A Critique of the Proposed Prototype Rating System for Personality D... Read more »

Skodol AE, Bender DS, Morey LC, Clark LA, Oldham JM, Alarcon RD, Krueger RF, Verheul R, Bell CC, & Siever LJ. (2011) Personality Disorder Types Proposed for DSM-5. Journal of personality disorders, 25(2), 136-69. PMID: 21466247  

Krueger RF, Eaton NR, Clark LA, Watson D, Markon KE, Derringer J, Skodol A, & Livesley WJ. (2011) Deriving an Empirical Structure of Personality Pathology for DSM-5. Journal of personality disorders, 25(2), 170-91. PMID: 21466248  

  • April 9, 2011
  • 12:38 PM

who’s afraid of the big, bad alien invaders?

by Greg Fish in weird things

Another day, another proposed solution to the Fermi Paradox, which asks where are all the aliens if the skies are just filled with extraterrestrial empires. Yesterday, my good frienemies at the arXiv blog shone a light on a paper by a quantum theorist which tackles the possible interactions between alien species from evolutionary points of [...]... Read more »

Adrian Kent. (2011) Too Damned Quiet?. n/a. arXiv: 1104.0624v1

  • April 9, 2011
  • 12:11 PM

Disorder promotes stereotyping

by William Lu in The Quantum Lobe Chronicles

Xenophobic exclusion has been ubiquitous throughout history. However, the explanation of such a phenomenon has been little understood. Interesting research conducted by Stapel and Lindenberg published in the latest Science has brought us closer to some answers. They found that people who are in a disordered environment (e.g. unclean subway station) exhibit greater discriminatory behavior (e.g. decision to sit further away from a black person compared to a white person). The authors suggest that when the brain faces disorder there is an equal need for order. One way to reach order is through stereotyping. It's the brain's way of making sense of the world. Too bad it doesn't work all the time.Stapel DA, & Lindenberg S (2011). Coping with chaos: how disordered contexts promote stereotyping and discrimination. Science (New York, N.Y.), 332 (6026), 251-3 PMID: 21474762... Read more »

  • April 9, 2011
  • 10:32 AM

The Meaning of Mastodon Tusks

by Laelaps in Laelaps

Until recently, I did not fully appreciate fossil teeth. Their significance for identifying species and narrowing down the general diet of extinct animals was obvious, but I didn’t understand that teeth also hold intricate records of an individual animal’s life. Tiny pits and scratches on enamel can reveal what a creature was eating around the [...]... Read more »

  • April 9, 2011
  • 05:25 AM

Detecting pathogens in medieval Venice

by Michelle Ziegler in Contagions

Medieval Venice was a trading empire, one of the busiest ports of the late medieval world. As a hub of commerce waves of plague visited and revisited Venice in 1348, 1462, 1485, 1506, 1575-1577, and 1630-1632 with the last two producing mortality rates around 30% of the population (Tran et al, 2011). As we all [...]... Read more »

Fournier PE, Ndihokubwayo JB, Guidran J, Kelly PJ, & Raoult D. (2002) Human pathogens in body and head lice. Emerging infectious diseases, 8(12), 1515-8. PMID: 12498677  

Foucault C, Brouqui P, & Raoult D. (2006) Bartonella quintana characteristics and clinical management. Emerging infectious diseases, 12(2), 217-23. PMID: 16494745  

  • April 9, 2011
  • 05:00 AM

How old am I?

by Sean Roberts in A Replicated Typo 2.0


It’s my birthday!  But how old am I?  Well, that’s not such a straightforward question.  Even a seemingly well-defined concept such as age can be affected by cultural factors
First, my age in years is a bit of an estimate of the actual amount of time I’ve been alive, due to leap-years etc.  Second, a year is . . . → Read More: How old am I?... Read more »

Knodel J, & Chayovan N. (1991) Age and birth date reporting in Thailand. Asian and Pacific population forum / East-West Population Institute, East-West Center, 5(2-3), 41. PMID: 12343437  

  • April 9, 2011
  • 02:36 AM

Liberals Are Conflicted and Conservatives Are Afraid

by The Neurocritic in The Neurocritic

This sums up the basic conclusion of a new study on political orientation and brain structure by Ryota Kanai, Tom Feilden, Colin Firth and Geraint Rees in the journal Current Biology. Yes, that Colin Firth...Colin Firth's Speech during the 2011 Academy Awards. Firth won Best Actor for The King's Speech.Why are Colin Firth and Tom Feilden, both listed with BBC Radio 4 affiliations, authors on this paper? Let's go back to Tuesday, 28 December 2010 and two pieces that appeared on the BBC website.Politics: Brain or background?Science correspondent Tom Feilden: "What started out as a bit of fun has turned into quite a significant piece of science."Scientific research commissioned by this programme on behalf of our guest editor, Colin Firth, has shown a strong correlation between the structure of a person's brain and their political views. You can also listen to a brief audio clip of Feilden discussing the study at the link above. Firth actually commissioned Professor Geraint Rees at University College London to obtain structural MRI scans from two diametrically opposed politicians: conservative MP Alan Duncan (a member of the Conservative Party) and liberal MP Stephen Pound (a member of the Labour Party).Feilden then asks a question that is unanswerable from studying brain structure in adults: "Are political beliefs learnt, the product of experiences in our environment, or 'hard wired' in the brain?" Since a comparison of n=1 liberal versus n=1 conservative is not scientifically valid, Rees went back to a database of MRI scans from UCL students and asked these participants about their political beliefs. Feilden then discussed the results before the paper had been formally submitted for publication [according to the journal website, the paper was received by Current Biology on 11 January, 2011]. Briefly, he said that the gray matter of the anterior cingulate cortex was thicker among the liberal or left wing participants while the amygdala was much larger in those who identified as conservative or right wing."But is it cause and effect?" asks an interviewer. Rightfully so. Correlation does not equal causation. Then there's the claim that the structural brain variation means the political differences are "hard wired". The observed anatomical differences mean no such thing. Any experience will change the brain in some way, and repeated patterns of behavior, whether it's learning to juggle or voting conservative due to a certain set of core beliefs, can alter the brain. Nonetheless, we have the following headlineAre political beliefs hard-wired?Tom Feilden| 08:10 UK time, Tuesday, 28 December 2010"Give me the child until he's seven and I'll give you the man."It's clear from their motto that the Jesuits are firmly in the acquired camp when it comes to whether our political beliefs and values are learned or hard wired from birth: the product of experience rather than genetics.But is that true? ...along with the eventual admission:Although the results do show that political belief is reflected in the physical structure of the brain it's not clear which comes first. Whether the structure of the brain shapes political belief or political belief leads to the differential development of brain structure.All right, that was a media stunt, you say -- but how about the peer reviewed paper (Kanai et al., 2011)?A total of 90 healthy middle-class to upper-class participants (mean age = 23.5 yrs) underwent MRI scanning and [later?] filled out a very brief questionnaire on their political views:Participants were asked to indicate their political orientation on a five-point scale of very liberal (1), liberal (2), middle-of-the-road (3), conservative (4), and very conservative (5). ... Because none of the participants reported the scale corresponding to very conservative, the analyses were conducted using the scales of 1, 2, 3, and 4.If I'm not mistaken, no special effort was made to recruit very conservative participants, because the study was conceived after the MRIs were obtained.As reported by Feilden, being liberal was associated with a larger anterior cingulate whereas being conservative was associated with a larger right amygdala1 (see Figure 1 below).Figure 1 (Kanai et al., 2011). Individual Differences in Political Attitudes and Brain Structure. (A) Regions of the anterior cingulate where gray matter volume showed a correlation with political attitudes are shown overlaid on a T1-weighted MRI... A statistical threshold of p < 0.05, corrected for multiple comparisons, is used for display purposes. The correlation (left) between political attitudes and gray matter volume (right) averaged across the region of interest (error bars represent 1 standard error of the mean, and the displayed correlation and p values refer to the statistical parametric map presented on the right) is shown. (B) The right amygdala also showed a significant negative correlation between political attitudes and gray matter volume. Display conventions and warnings about overinterpreting the correlational plot (left) are identical to those for (A).The results were based on measurements of gray matter density in these two specific structures. How were they chosen? First, the anterior cingulate was selected based on the finding of Amodio et al. (2007) that......the amplitude of event-related potentials reflecting neural activity associated with conflict monitoring in the anterior cingulate cortex (ACC) is greater for liberals compared to conservatives. Thus, stronger liberalism is associated with increased sensitivity to cues for altering a habitual response pattern and with brain activity in anterior cingulate cortex.I had issues with this interpretation of the Amodio et al. study in 2007, which I will summarize here. One problem was attributing the observed results to political viewpoint and not to other factors. The study used EEG recordings, specifically event-related potentials. The ERP brain waves reflect electrophysiological activity recorded remotely from the scalp. While it's great for determining the temporal parameters of neural activity, it's not so great at determining where the activity is located in the brain.One brain wave of inter... Read more »

Ryota Kanai, Tom Feilden, Colin Firth, Geraint Rees. (2011) Political Orientations Are Correlated with Brain Structure in Young Adults. Current Biology. info:/10.1016/j.cub.2011.03.017

  • April 8, 2011
  • 10:45 PM

Yes We C(r)an(berry)!

by James Byrne in Disease Prone

That title is awful I know but I'm tired. Cut me some slack :)  I ran into a something that I have heard about before but assumed was rubbish and never really looked into it properly. A friend of mine insisted it was the case so I looked it up and I have to say, I was a little surprised.

So this is what cranberries look like. I never knew.
Cranberry juice is apparently very good at prevent urinary tract infection, particularly in women. There have been a few studies approaching it from different angles but, disappointingly, the studies all use different types of cranberry product, different doses and dosing techniques but despite all this the message seems to be pretty clear. Cranberries prevent urinary tract infections kicking in.
Before we can consider how this occurs its important to define what we are talking about. Urinary tract infections or UTIs are generally caused by a strain of Escherichia coli called Uropathogenic E. coli (UPEC) and it gets there by moving from the colon…ew. For this reason men rarely have to worry about them while they can be a chronic problem for women around the world, however the insertion of urinary catheters is a major risk factor for both genders. Clinical symptoms include burning sensation during urination and cloudy urine but these are only really evident once the bacteria have ascended the urethra into the bladder causing urethritis and cystitis respectively. If you want to feel real pain however let the little bastards work their way into your kidneys where kidney infection (or pyelonephritis) results in the above symptoms plus back pain and fever and the possibility of systemic spread.
So the first step in the infective process is generally stable colonisation of the colon. This step is often overlooked but without a source of UPEC it’s hard to get a proper infection going. The next step is invasion of the vaginal microbiota. Not an insignificant task since the vaginal niche is normally fully occupied by lactobacilli and other innocuous strains. Only once this has occurred can the UPEC ascend the urethra.

Having ascended the urethra the UPEC are not in the free and clear because the bladder and urethra have a formidable barrier to infection, the waterfall of flushing, cleansing urine that washes away all in its path. To overcome this UPEC have developed powerful adhesins, proteins used adherence of the bacterium to a surface and in this case specifically to the urinary epithelial tissue.
Adhesins are found in most pathogenic bacterial species but the array and strength of the UPEC adhesins is staggering. Among the most important adhesins produced by the UPEC are the pili. Pili are hair-like structures on the bacterial surface that are often capped with sticky (in the molecular sense) ends that facilitate adhesion. Importantly for UPEC possessing three different sticky caps (S, P and Type 1 pili) increases the chances of binding.
The S pili tend to be more important for adhesion outside of the gentio-urinary tract and so may play a part in systemic spread. In the urine however these pili bind the mannose filled protein uromodulin. Because of this S pili are called mannose sensitive pili and its thought that the ability to bind uromodulin, the most abundant protein in urine, possibly results in bacterial clumping and this allows a better opportunity for the P and Type 1 pili to do their thing. These two pili are responsible for the binding in the urethra and bladder.
Initially the Type 1 pili bind mannose sugars on the surface of the bladder cells allowing the bacteria to get some traction on the bladder/urethra walls before the P pili bind to a different sugar group to cement the interaction. The ability of P pili to bind non-mannose sugars has earned them the alternative title mannose resistant pili whereas type 1 pili are grouped with the mannose sensitive S pili.

The pili are the hairy bits on the picture of E. coli. The paper this pic is from is referenced at the bottom.
Once adhered to the host surface the UPEC can invade the epithelial cells but the bladder’s defence against this is to kick those invaded cells into the urine. A good defence strategy but it may contribute to tissue damage in the urinary tract when infections are recurrent. Also it seems some bacteria can prevent this expulsion of the cell they have invaded and in doing so remain as a reservoir of infection out of the way of the immune system and most antibiotic treatments.
Invasion does not always occur and instead some UPEC strains are able to release toxins directly onto the host epithelial surface due to the close interaction between bacterium and host. These toxins, as well as one of my boss’s favourite little molecules lipopolysaccharide (LPS) cause the inflammation that goes with the UTI.
So that’s the UTI side of things but where does Cranberry juice come into this story?
Cranberries (Vaccinium macrocarpon if you don’t mind) together with blueberries and Concord grapes constitute the only native fruit species to the US and Canada. Bet you didn’t know that, or maybe you did but I didn’t. In any case often the best way to work out what the native flora is capable of you have to look back to the indigenous peoples and, surprise surprise, Native Americans have known about and utilised the medicinal properties of cranberries for many years. Commonly used in different preparations to treat blood disorders, stomach issues, liver trouble and fevers.
By the 1880’s people were trying to work out what was doing what with cranberries and some German researchers found benzoic acid in cranberries. Then as now it was known to be a potent antiseptic and was included in a number of medicines and topical anti-bacteria treatments. This observation set researchers down the wrong path from the get go as the real power of cranberries lies in other activities of other compounds.
Continuing research into the antibacterial properties of cranberries found the benzoic acid was converted to hippuric acid, another antibacterial agent that also has a role in acidifying the urine. Everyone thought they were onto a winner. A powerful antibacterial compound excreted in the urine because you ate some cranberries. This is open and closed right? Well…

Could I be any clearer... Read more »

  • April 8, 2011
  • 08:19 PM

100 sextillion stars wasn't enough

by Cyc in The Rantings of a Gothic Atheist

100 sextillion. Or if you like visual aids 100,000,000,000,000,000,000,000. This has been the estimated number of stars in the visible universe. Or at least it was until recently. A study by a team headed by Van Dokkum, using Hawaii's Keck Observatory, have just tripled this number.

Using the spectrometer at the Keck Observatory, the team analyzed eight near by elliptical galaxies. When it comes to galaxies, the term 'near by' can seem a bit misleading. In this case they were between around 50 and 300 million light years away. In these, the largest of galaxies, the team went looking for Red Dwarfs, relatively small stars with long life-spans. In the case of stars, the smaller the star, the longer the life span. This is due to the effects of gravity spurring on the fusion that rules the lives of stars, with a size of .075 solar masses, this makes for an increadibly long life. Due to the vast distances involved, the signatures of Red Dwarfs were previously impossible to detect. To get around this problem, an estimate of the number of Red Dwarfs in our own galaxy was taken and this number was extrapolated to other galaxies.

In our own galaxy, the Milky Way, there are about 100 Red Dwarfs for every other star. However this new data revealed that the far larger elliptical galaxies had closer to 1,000 Red Dwarfs for every one other type star. In an article at, Van Dokkum stated:

Elliptical galaxies are some of the largest galaxies in the universe. The largest of these galaxies were thought to hold more than 1 trillion stars (compared with the 400 billion stars in our Milky Way). The new finding suggests there may be five to 10 times as many stars inside elliptical galaxies than previously thought, which would triple the total number of known stars in the universe, researchers said.
Besides the obviously implications about the prevalence of star formation in massive galaxies, there are two other important extrapolations from this data. This first being planet formation. It is already known that planets can and do form around Red Dwarfs. Recently a Venus like "Super-Earth" was found orbiting one of these small stars. With such a grand increase in the number of available stars, the number of planets is increased dramatically as well. While there is still some debate as to the habitability of planets orbiting Red Dwarfs, some hope is given in their long, stable lives. Where as our own star, Sol, has a life span around 10 billion years, the average Red Dwarf is expected to maintain fusion for 10 trillion years.

The next repercussion has to do with a quandary involving Dark Matter. Before this discovery, the amount of Dark Matter in elliptical galaxies was thought to be higher than in other types of galaxies. This was detected by the strong gravitational lensing seen around such galaxies. Gravitational lensing being the effect of light being bent around massive objects, the greater the bend, the more massive the object. But with the mass of the increased number of Red Dwarfs factored in, the amount of Dark Matter seems to be more along the expected amounts.

van Dokkum, P., & Conroy, C. (2010). A substantial population of low-mass stars in luminous elliptical galaxies Nature, 468 (7326), 940-942 DOI: 10.1038/nature09578

... Read more »

  • April 8, 2011
  • 07:04 PM

Impulsive? Reduce your risk – go to Alcoholics Anonymous

by PeaPod in Binge Inking

Impulsivity (or the tendency to act first and think later) is a common trait in people with alcohol and drug dependence. In a paper published in the Journal of Studies on Alcohol and Drugs, researchers posed the question: would going to AA and professional treatment reduce impulsive behaviour in individuals with alcohol use disorders? Here's what they found...... Read more »

  • April 8, 2011
  • 02:45 PM

Disorder increases Stereotyping and Discrimination

by dj in Neuropoly

A slew of studies over the past few years have looked at how some seemingly innocuous contextual and environmental factors can influence cognitive and behavioral processes. In a study just published in Science, researchers from the Netherlands showed that disordered contexts promote stereotyping and discrimination. The premise of the study was derived from previous work [...]... Read more »

Diederik A. Stapel1 and Siegwart Lindenberg. (2011) Coping with Chaos: How Disordered Contexts Promote Stereotyping and Discrimination. Science, 332(6026), 251-253. info:/DOI: 10.1126

Inbar, Y., Pizarro, D., Knobe, J., & Bloom, P. (2009) Disgust sensitivity predicts intuitive disapproval of gays. Emotion, 9(3), 435-439. DOI: 10.1037/a0015960  

  • April 8, 2011
  • 02:02 PM

Life After Death At Yellowstone: An Interview with Josh Miller

by Andrew Farke in The Open Source Paleontologist

In my last post, I introduced a ground-breaking study recently published in PLoS ONE, that shows how we can infer long-term trends in animal populations just from their bones. This work has big implications for ecology, conservation, and public policy, and is also a really neat piece of science. For this post, I talked to the author of the study, Josh Miller, about his work and some of the tidbits that didn't make it into the paper.Yellowstone NP gets a lot of visitors, and you surely must have had some interactions with them during your fieldwork. How did they react to what you were doing? JM: I work in areas that are generally well off trail and in places most Yellowstone visitors just don't see. Over the years, there are have been very few times when tourists actually ever saw my teams conducting our bone work. Most of the time, conversation with the public occur in the evenings back at camp. We generally use the public campgrounds for our homebases and my research will often come up in conversation with tourists. When folks learn what my teams and I are up to, they are always very interested and ask lots of questions. Our National Parks are an important resource, and I think people like to be reminded of their biological and scientific value. At the same time, I think it gives folks a way of looking at Yellowstone in a new and exciting way. I know lots of people who talk to us one day and keep an eye out for bones the next.Miller studying bone survey data sheets on Northern Range, Yellowstone National Park. Photo by Scott Rose.You looked at hundreds of bones during your survey. Was there any particular specimen that stuck out in your mind? What about it was interesting?JM: I looked at over 20,000 bones during my work in Yellowstone. And you are right, there are a few that really stand out. Some of the most memorable bones are those of animals with severe bone maladies. In some individuals we found severe arthritis or broken bones that didn’t heal properly. Other memorable bones include rare and unusual species. One of the most exciting finds was the skull of a mountain lion. We just stumbled upon on it one afternoon walking from one transect to another. This beautiful rounded huge cat skull just lying in the grass staring up at us –a rare and amazing site.This paper focused on bones from large animals, but surely there are a lot of small animal bones out there too - rodents, bats, rabbits, etc. Do you think they would show a similar correlation over time between abundance in life and death? Or are the taphonomic effects too different between large and small animals to expect the same pattern? JM: Stay tuned! I kept careful attention to the bones of the small mammals we found. My bone survey teams were amazingly good at finding bones of all shapes and sizes (from bison skulls to limb bones of squirrels). One of the challenges, unfortunately, is the lack of high-quality data on the living populations in Yellowstone. One thing I'll say at the moment, however, is that the record of small-bones is surprisingly rich and diverse on the Yellowstone landscapes.I see that you used the open source stats program R to do your data analysis. Was this something you picked up just for your dissertation work? Why did you choose R over some of the other commercial packages that are out there?JM: I was introduced to R during the early days of my graduate work. R is a very powerful statistics language, in part, because of the large community of scientists and academics that use R and contribute to its ever-expanding utility. Another reason I use R is that I can completely control all aspects of the analysis. In canned programs, much of the analysis sits under a black box and uncovering exactly how the data were analyzed can be very difficult. But most of all, R just fits how I do science.Thank you for your time, Josh!CitationMiller, J. (2011). Ghosts of Yellowstone: Multi-Decadal Histories of Wildlife Populations Captured by Bones on a Modern Landscape PLoS ONE, 6 (3) DOI: 10.1371/journal.pone.0018057Note: I'm an academic editor at PLoS ONE, but had no role in the handling of this paper.... Read more »

  • April 8, 2011
  • 12:25 PM

Microbiome Studies: We Are More than the Sum of our Parts

by Isobel in Promega Connections

What if you could help protect yourself from certain diseases by populating your gut with “good” bacteria, or selectively getting rid of “bad” ones? Two news articles suggesting this possibility caught my eye this week. The articles both summarized results from the microbiome project–a research effort geared towards developing a deep understanding of how the [...]... Read more »

Wang, Z., Klipfell, E., Bennett, B., Koeth, R., Levison, B., DuGar, B., Feldstein, A., Britt, E., Fu, X., Chung, Y.... (2011) Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature, 472(7341), 57-63. DOI: 10.1038/nature09922  

  • April 8, 2011
  • 12:00 PM

Is it time for a sustainable pet movement?

by Southern Fried Scientist in Southern Fried Science

The world is rapidly approaching 7 billion people and the challenges of food supply, security, and sustainability will, along with climate change, be the defining issues of the 21st century. While the issues of the wealthiest nations revolve around the quality of our food, the environmental impact or our farming practices, and the value we place [...]... Read more »

Sleeman JM, Keane JM, Johnson JS, Brown RJ, & Woude SV. (2001) Feline leukemia virus in a captive bobcat. Journal of wildlife diseases, 37(1), 194-200. PMID: 11272497  

Roelke ME, Forrester DJ, Jacobson ER, Kollias GV, Scott FW, Barr MC, Evermann JF, & Pirtle EC. (1993) Seroprevalence of infectious disease agents in free-ranging Florida panthers (Felis concolor coryi). Journal of wildlife diseases, 29(1), 36-49. PMID: 8445789  

  • April 8, 2011
  • 11:57 AM

Memory distortions: Not just for long-term memories

by Audrey Lustig in ionpsych

We often remember things by relying on the overall gist of an event—for example, instead of storing every detail about our last birthday, we tend to remember abstract things like “I had a fun party” or “I was in a grumpy mood because I felt old.” This strategy allows us to remember more things about an event, but there’s one major drawback: by storing memories based on gist, we actually change how we remember the event. This happens because we are biased to remember things that are consistent with our overall summary of the event. So if we remember the birthday party was “super fun” overall, we’ll exaggerate how we remember the details—the average chocolate cake is now “insanely good”, and the 10 friends who were there becomes a “huge crowd.” One of the factors that could contribute to this distortion is time; as you forget the details of an event, there’s more room for gist to change how you remember things. But you would remember the details of an event immediately afterward, right?... Read more »

Brady TF, & Alvarez GA. (2011) Hierarchical encoding in visual working memory: ensemble statistics bias memory for individual items. Psychological science : a journal of the American Psychological Society / APS, 22(3), 384-92. PMID: 21296808  

  • April 8, 2011
  • 11:14 AM

The great (big) American lawn

by Tim De Chant in Per Square Mile

Spring is descending on the United States. Buds on trees and shrubs are swelling, and brittle brown grass is beginning to show green signs of life. As people put away their snow shovels and dust off their lawn mowers, it’s also a good time to take stock of the American lawn, which plays a starring [...]... Read more »

  • April 8, 2011
  • 11:10 AM

The N1 Component in Prereading Children

by Livia in Reading and Word Recognition Research

Accessibility: Intermediate-Advanced

Just to recap from the last article, the N170 is an ERP component that differentiates between words and symbol strings in normal reading adults. This the specialization developed after learning to read, or does it have something to do with the visual properties of symbols?

Maurer and colleagues tested pre-reading kindergartners to see whether the specialization is there before they learn to read. They had kids perform the same task as adults (looking at a series of words, pseudowords, symbol strings, and pictures).

They found several things:

1. Adults again had the same N170 (called N1 in this paper), which was stronger for words than symbols.

2. Kids also had an N1, but it was later, had a larger amplitude, and most importantly, did not distinguish between words and symbols, suggesting that this N1 specialization stems from experience with words.

3. Some of the kids, the ones with high letter knowledge, did have an N1 that differentiated between letters and symbols. However, the pattern was different from adults. While adults had the strongest effect on the left side of the brain, these children showed an effect on the right side.

So in conclusion, the N1 specialization seems to be related to reading. However, there seem to be some intermediate steps in the development of the specialization. At least in an early stage, the right hemisphere is involved, and then the processing becomes more left lateralized.

Maurer U, Brem S, Bucher K, & Brandeis D (2005). Emerging neurophysiological specialization for letter strings. Journal of cognitive neuroscience, 17 (10), 1532-52 PMID: 16269095

What is it that transforms a page full of words into an experience that moves us and leaves us changed? K. Okada From Words to Brain

... Read more »

Maurer U, Brem S, Bucher K, & Brandeis D. (2005) Emerging neurophysiological specialization for letter strings. Journal of cognitive neuroscience, 17(10), 1532-52. PMID: 16269095  

  • April 8, 2011
  • 10:15 AM

Canada’s Children’s Fitness Tax Credit – The Rich Get Richer?

by Travis Saunders, MSc, CEP in Obesity Panacea

As many of our readers will know Canada is in the midst of an election campaign and the major parties are putting out a number of policy ideas on a daily basis. One idea proposed by Conservative leader Stephen Harper was to expand the Canadian Children’s Fitness Tax Credit (CFTC).  As it currently stands, the CFTC offers a $500 non-refundable tax credit that parents can receive by enrolling their child in an approved physical activity program.  If I understand it correctly, this means that if your income is $50,000, claiming this credit would effectively reduce your taxable income to $49,500.
While a $500 tax credit may sound pretty large, at the end of the day parents only save a maximum of $75 per child (this saving can be increased by another $75 if the child has a disability).  And keep in mind that parents still need to be able to afford the full $500 fee up front – they don’t get the $75 saving until tax season.  So if Junior’s soccer fees come to $500 and you only have $425 dollars, you’re out of luck.  You need to be able to pay that full $500 fee and then wait until the following spring to have your tax-bill reduced by $75.
Mr Harper is proposing that the current CFTC be expanded to offer a $1,000 tax-credit per child, as well as offering a similar $500 tax-credit for adults (an important detail being that these credits won’t be until the budget is balanced… which is projected to be 2015 at the earliest).  This would mean that parents could now save up to $150 per child, and an additional $75 for themselves…. once the budget is balanced.
These types of tax-credits seem to be catching on with politicians on both sides of the political spectrum as similar credits have been enacted or expanded by the Liberal government here in Ontario, the New Democratic Party in Manitoba, the Progressive Conservative Party in Nova Scotia, the Yukon Party in the Yukon and the Saskatchewan Party in (you guessed it) Saskatchewan (one key difference for the Saskatchewan program being that it is fully refundable).  Similar credits are rumored to be in the works in both Australia and the USA as well.
So, since are these types of tax-credits seem to be increasing in popularity among politicians, and given the limitations described above, is there any evidence that they actually increase physical activity levels? Luckily, a recent paper by John Spence and colleagues at the University of Alberta looked at this exact question.
In this new paper, Dr Spence et al. surveyed a representative sample of 2,135 Canadian adults to ask them if they were aware of the CFTC, if they had claimed it/planned to claim it, and whether they believed that the CFTC led to their child being more involved in physical activity programs.
I have inserted 2 figures of their most telling results below.  I graphed it twice and wasn’t sure which way did a better job of breaking it down, so I have included both.
Figure 1.  Result by Income Quartile (Q1 = lowest income, Q4 = highest income).
Data from Spence et al., 2010
Figure 2. Results by question.
Data from Spence et al. 2010
Not surprisingly, both graphs suggest that the individuals with a higher income were much more likely to report having a child involved with organized physical activity (68% in Q4 vs 40% in Q1).  Similarly, these high income individuals were much more likely to have knowledge of the CFTC, and have claimed it in 2007 or plan to claim it in 2008.  The proportion of individuals in Q3 and Q4 who claimed the CFTC in 2007 was double the proportion of individuals in Q1. The authors also note that among those who claimed the CFTC in the past only 15% said that it led to their children being more involved in organized physical activity.
Given these findings Dr Spence and colleagues conclude that:
More than half of Canadian parents with children have claimed the CFTC. However, the tax credit appears to benefit the wealthier families in Canada.
Clearly, if increasing enrollment in organized physical activity is the goal, this type of tax-credit seems unlikely to make much of a difference.  Based on the results of this paper, it seems that the current CFTC is of benefit to people who can already afford to put their kids in organized sport, but is of little use to the children who need it the most.
I would argue that for the same amount of money, we could get far more children involved in sport by funding programs directly, or by working out a system whereby children from  low-income families simply have to pay lower registration fees compared to those from high-income families.  I know that many sports programs, such as the Fredericton Youth Hockey Association, already have systems like this in place by reducing registration fees and/or providing free equipment to children in financial need.  If getting kids involved in organized activities is the goal then I would argue that this type of program is much more likely to make an actual difference than the fitness tax credits that are popping up around the country (Full disclosure – my dad is heavily involved with the FYHA and its program for kids with financial need, although I’d be a fan of the program even if he wasn’t).
All that to say that while expanding the CFTC isn’t necessarily a bad thing, it’s probably not going to do much to increase enrollment in organized physical activity among those who need it most.
For an excellent explanation of why the CFTC isn’t terribly effective from an economic perspective, I suggest this Globe and Mail article by Kevin Milligan.
Hat tip to Meghann Lloyd for letting me know about the plans to expand the CFTC (if/when the budget is balanced).
Spence, J., Holt, N., Dutove, J., & Carson, V. (2010). Uptake and effectiveness of the Children’s Fitness Tax Credit in Canada: the rich get richer BMC Public Health, 10 (1) DOI: 10.1186/1471-2458-10-356
... Read more »

  • April 8, 2011
  • 10:13 AM

Life After Death at Yellowstone

by Andrew Farke in The Open Source Paleontologist

Taphonomy - the study of what happens to an organism after it dies - is integral to reconstructing the past. Perhaps the most important lessons come in inferring ecological interactions. Did that group of animals live and die together, or were they jumbled long after death? Were all of those shark teeth with the plesiosaur bones from a feeding frenzy, or just a fluke of currents? How closely does a set of fossils represent the relative abundance of the different species in the quarry? Such examples are numerous, and thus we commonly think of taphonomy as a study in deep time. This is certainly true, but also certainly incomplete. In fact, some of the most ground-breaking taphonomic work has been done in contemporary ecosystems. Kay Behrensmeyer, for instance, has spent decades studying bone accumulations in Kenya, and a 1927 work by Johannes Weigelt (complete with photos of dead cattle) is still considered a classic.A new study by paleontologist and taphonomist Josh Miller, just published in PLoS ONE, shows some of the great insights that can arise from looking at taphonomy in modern settings. Josh and his field assistants trekked through Yellowstone National Park (one of the western USA's oldest and best-known parks), cataloging the identity and physical condition of every animal bone sitting out on the surface (an elk skeleton from the project is shown at right; photo courtesy of and copyright Josh Miller). Using these data, Josh found that you can actually infer the major ups and downs of animal populations from their old bones. This is quite exciting, not just from a gee-whiz factor, but because it may be possible to infer population trends for areas where historical surveys are absent or spotty. Such data are important not only for ecologists, but for informed public policy. It sounds magical, so how was the study done?Based on other studies (in combination with radiometric dating), it's known that bones in excellent condition usually came from animals that died only recently, whereas bones in crummy condition are from animals that died longer ago. By using the condition of the bones as a proxy for time since death, Josh estimated how long the various bones of various animals had been around. Then, based on the bone ages, he estimated the relative population of each type of animal a given number of years ago. We have very good wildlife census data for Yellowstone, and it turns out that estimates from the bones match the "real" values quite nicely. Boom years for animals (such as elk) mean lots of bones going into the system, bust years mean few bones, and these trends shows up in bone surveys.You can read all about it at PLoS ONE, or here, here, and here. I recently talked to Josh to get a few behind-the-scenes tidbits. Stay tuned for the interview later today!CitationMiller, J. (2011). Ghosts of Yellowstone: Multi-Decadal Histories of Wildlife Populations Captured by Bones on a Modern Landscape PLoS ONE, 6 (3) DOI: 10.1371/journal.pone.0018057Note: I'm an academic editor at PLoS ONE, but had no role in the handling of this paper.... Read more »

  • April 8, 2011
  • 10:02 AM

Colour terms and national flags

by Sean Roberts in A Replicated Typo 2.0

Today, I wondered whether the number of basic colour terms a language has is reflected in the number of colours on its country’s flag. The idea being that a country’s flag contains colours that are important to its society, and therefore a country with more social tools for discussing colour (colour words) will be more likely to put more colours on its flag. It was a long shot, but here’s what I found:... Read more »

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