Post List

  • October 18, 2010
  • 06:52 PM

The Curious Tale of a Far-Flung Whale

by Laelaps in Laelaps

When marine biologists first spotted the humpback whale AHWC no. 1363, there did not appear to be anything remarkable about her at all. Seen with another female on the Abrolhos Bank off the coast of Brazil on August 7th, 1999, the whale simply stuck around long enough for the scientists to snap a few photographs [...]... Read more »

  • October 18, 2010
  • 05:21 PM

New in PLoS ONE: Citation rates of self-selected vs. mandated Open Access

by Martin Fenner in Gobbledygook

PLoS ONE today published a paper very relevant to Open Access Week (which started today):
Gargouri Y, Hajjem C, Larivière V, Gingras Y, Carr L, Brody T, Harnad S. Self-Selected or Mandated, Open Access Increases Citation Impact for Higher Quality Research. PLoS ONE. 2010;5(10):e13636+. doi:10.1371/journal.pone.0013636.
The paper studied the citation rates of papers from four institutions with the longest-standing self-archiving mandate: Southampton University, CERN, Queensland University of Technology and Minho University. The mandates (instituted between 2002 and 2004) increased the rate of self-archiving in the respective institutional repositories from around 15% to 60%:

Fig 1. Open Access Self-archiving percentages for institutions with self-archiving mandates compared to non-mandated, self-selected controls. doi:10.1371/journal.pone.00136363.g001
The authors then compared the citation rates of self-archived papers from the four institutions published in non-Open Access (OA) journals (mandated OA) to matched papers from the same non-OA journal, volume and year (non-OA). 15% of the latter papers were also available from repositories (self-selected OA). Overall the study examined the citations of 27,197 papers from 1,984 non-OA journals. The study also looked at the influence of other factors that affect citation rates, e.g. article age, journal impact factor or number of references.
The main results of the study are that OA articles are cited more frequently than non-OA articles and that there is no difference in citation rates between mandated and self-archived articles. The authors conclude that OA articles are cited more often not because of self-selection (articles with higher impact more likely become OA), but because of readers cite OA articles more often.
The study is an effort to better understand if and why OA papers are cited more often, the so-called OA Advantage. Unfortunately I feel that the paper comes a little short. Yes, they did a very detailed analysis of the citation behavior, and take into account important cofactors. But the reader is left with the impression that mandatory self-archiving of post-prints in institutional repositories is the only reasonable Open Access strategy, and the introduction and discussion accordingly leave out some important arguments.
The authors fail to mention that not all studies show a citation advantage for OA articles (e.g. the randomized controlled trial by Davis PM et al. 2008), and they only look at self-archiving in institutional repositories (green OA). Not only are there important disclipline-specific repositories such as PubMed Central and ArXiv, but of course also OA journals such as PLoS ONE that published the study (gold OA). And the study only discussed archiving of articles after peer review, even though archiving of preprints is a popular strategy in high-energy physics and related disciplines (and here the self-archiving rate is close to 100%). I also don’t see a discussion of why the self-archiving rate of post-prints in institutions with a mandate is 60% and not close to 100%. And what is wrong if archiving rates are only around 15% if it is left to the researchers to decide? Finally, there are many reasons other than citation rates that make OA worthwhile, including access to the literature for those not working in academic institutions (and maybe never citing a paper), and work that uses the OA literature in new and exciting ways that go beyond citations. For me personally, the OA advantage is much more in these two aspects than in the citation rates of papers.
For me Open Access week is an opportunity to celebrate what has been achieved over the years. But it is equally important to look at the road ahead. There is no “one size fits all” solution for Open Access, and we shouldn’t look away from the things that aren’t working, and the solutions that haven’t been found yet.
Gargouri, Y., Hajjem, C., Larivière, V., Gingras, Y., Carr, L., Brody, T., & Harnad, S. (2010). Self-Selected or Mandated, Open Access Increases Citation Impact for Higher Quality Research PLoS ONE, 5 (10) DOI: 10.1371/journal.pone.0013636
... Read more »

  • October 18, 2010
  • 04:53 PM

Spreading Salmonella—hyper-replicating bacteria act as a reservoir for dissemination

by geekheartsscience in geek!

New research reveals how Salmonella enterica spread in the gut and gallbladder—a subpopulation of Salmonella primed for invasion rapidly replicate in the host cell cytosol such that bacteria-laden cells are extruded out of the epithelial-cell layer releasing invasive Salmonella into the gastrointestinal and biliary lumen. Leigh Knodler and colleagues write that other mucosal-dwelling pathogens could [...]... Read more »

Knodler, L., Vallance, B., Celli, J., Winfree, S., Hansen, B., Montero, M., & Steele-Mortimer, O. (2010) Dissemination of invasive Salmonella via bacterial-induced extrusion of mucosal epithelia. Proceedings of the National Academy of Sciences, 107(41), 17733-17738. DOI: 10.1073/pnas.1006098107  

  • October 18, 2010
  • 02:45 PM

Crabs expose colliding continents

by Lucas in thoughtomics

Every high school student now learns that plate tectonics slowly drive our continents in different directions. Since only the most uncontroversial scientific knowledge finds its way to high school text books, it’s hard to imagine that when the theory of continental drift was proposed by Alfred Wegener in 1912, it was firmly rejected by [...]... Read more »

  • October 18, 2010
  • 02:37 PM

Working and chronic pain

by Bronwyn Thompson in Healthskills: Skills for Healthy Living

If there is one aspect of chronic pain management that has received more attention than returning to work, I don’t know it! In 1995 when I started working at my current workplace, work was almost a dirty word. I was accused at one time of being a ‘Siberian workcamp’ Commandante because some people thought it … Read more... Read more »

Costa-Black, K., Loisel, P., Anema, J., & Pransky, G. (2010) Back pain and work. Best Practice , 24(2), 227-240. DOI: 10.1016/j.berh.2009.11.007  

  • October 18, 2010
  • 02:34 PM

There are more things in heaven and earth, cobber, than are dreamt of in your philosophy

by Alun in AlunSalt

Studying astronomy in culture should be simple. There’s only so much that is visible by the naked eye, and it follows predictable patterns. Modern astronomy means that we can reconstruct what was visible anywhere in the world in human history, within certain boundaries for errors. If we know what happens when, then studying a culture... Read more »

Clarke, P.A. (2007) An Overview of Australian Aboriginal Ethnoastronomy. Archaeoastronomy: The Journal of Astronomy in Culture, 39-58. info:/

  • October 18, 2010
  • 01:19 PM

Chopping bits out of the genome

by Lab Rat in Lab Rat

Generally bacteria genomes tend to be fairly minimal in the amount you can remove from them. Unlike eukaryotes, which can have whole swathes of genome that codes for very little, bacteria, with their limited space for a chromosome, need every gene they can get. They just don't have the space for unnecessary genes.Streptomyces bacteria, however, have bigger genomes and the luxary to invest in genes which are not strictly necessary for bacterial survival. These are called Secondary metabolite genes (as opposed to the necessary primary metabolites) and they code for genes that aren't strictly needed for survival, but instead form an arsenal of weapons for the Streptomyces to deploy. Most Strep are soil-based, and they need the ability to produce secondary metabolites (such as antibiotics) to fight off invading bacteria, and clear terratory to expand their growth into.What has recently been done (very ingeniously) is to remove the secondary metabolism genes from the bacterial species Streptomyces avermitilis creating essentially an 'empty' strep bacteria, that can grow and divide but not produce any of the secretory substances that strep are known for. The researchers managed to cut an entire 1.5Mb of DNA right out of the genome - helped by the fact that all the secondary metabolite genes cluster together on one side of the chromosome.They did this using a common molbio technique, the cre-lox system. "Lox" is an area of DNA and "cre" is the protein that very specifically cuts DNA at the Lox site - it acts like a pair of scissors. They put a Lox site on either end of the DNA that codes for secondary metabolites (using a techinque called recombination in order to attach the lox into the chromosome) along with the DNA for the Cre protein under an inducible promoter. Once the bacteria had grown, they activated Cre production, which then cut the unwanted DNA out of the bacteria. This technique was amazingly successful and is shown diagramatically below (picture from the reference):The avimitilis now contains no secondary metabolites at all, which makes a wonderful 'empty' system to use for studying how secondary metabolites are made. Genes from other bacteria, or even some of the removed genes, can be added back in, piece at a time, to see how much of the gene is necessary for metabolite production, and which regulatory pathways are the most important. Creating an empty cell also has potential implications for biotechnology, after all when trying to produce antibiotics you want the cell working as hard as possible just to produce your product, not wasting time and resources on other metabolites!I'm really impressed at this kind of large scale synthetic-biology. It may be an area I end up going into in the near future...---Komatsu M, Uchiyama T, Omura S, Cane DE, & Ikeda H (2010). Genome-minimized Streptomyces host for the heterologous expression of secondary metabolism. Proceedings of the National Academy of Sciences of the United States of America, 107 (6), 2646-51 PMID: 20133795... Read more »

Komatsu M, Uchiyama T, Omura S, Cane DE, & Ikeda H. (2010) Genome-minimized Streptomyces host for the heterologous expression of secondary metabolism. Proceedings of the National Academy of Sciences of the United States of America, 107(6), 2646-51. PMID: 20133795  

  • October 18, 2010
  • 01:00 PM

Riding the Spore Wind

by Moselio Schaechter in Small Things Considered

Sooner or later, but usually sooner, anyone dealing with fungi will have to deal with the issue of spore dispersal. Many fungi, mushrooms included, are a spore’s way of spreading spores through the environment. They do this in varied and universally ingenious ways. Spores, like mammalian sperm, are made in excess, which enhances the chances of some “making it.” Anybody who has made the spore print from a mushroom can attest to the large number of spores produced. This is true not only for the Basidiomycetes, to which most mushrooms belong, but also for the larger Ascomycetes, (the group that includes not only yeast but also most molds, as well as larger organisms such as the cup fungi).

For dispersal to be efficient, the spores must travel a certain distance from their place of origin. They are ejected with great force, sometimes challenging our belief.... Read more »

Roper M, Seminara A, Bandi MM, Cobb A, Dillard HR, & Pringle A. (2010) Dispersal of fungal spores on a cooperatively generated wind. Proceedings of the National Academy of Sciences of the United States of America. PMID: 20880834  

  • October 18, 2010
  • 12:23 PM

Internal coarse-graining of molecular systems

by evopapers in evopapers

Feret J, Danos V, Krivine J, Harmer R, & Fontana W (2009). Internal coarse-graining of molecular systems. Proceedings of the National Academy of Sciences of the United States of America, 106 (16), 6453-8 PMID: 19346467, PNAS page, Supporting Information.   Models of molecular dynamics suffer from combinatorial explosion: the phenomenon of an exponential number of [...]... Read more »

Feret J, Danos V, Krivine J, Harmer R, & Fontana W. (2009) Internal coarse-graining of molecular systems. Proceedings of the National Academy of Sciences of the United States of America, 106(16), 6453-8. PMID: 19346467  

  • October 18, 2010
  • 12:00 PM

Guest Post: The fine-structure constant is probably constant by Sean Carroll

by S.C. Kavassalis in The Language of Bad Physics

This is the first guest post on The Language of Bad Physics by Cosmic Variance‘s Sean Carroll.  This post is cross-posted on Cosmic Variance.
A few weeks ago there was a bit of media excitement about a somewhat surprising experimental result. Observations of quasar spectra indicated that the fine structure constant, the parameter in physics that describes the strength of electromagnetism, seems to be slightly different on one side of the universe than on the other. The preprint is here.
Remarkable, if true. The fine structure constant, usually denoted α, is one of the most basic parameters in all of physics, and it’s a big deal if it’s not really constant. But how likely is it to be true? This is the right place to trot out the old “extraordinary claims require extraordinary evidence” chestnut. It’s certainly an extraordinary claim, but the evidence doesn’t really live up to that standard. Maybe further observations will reveal truly extraordinary evidence, but there’s no reason to get excited quite yet.
Chad Orzel does a great job of explaining why an experimentalist should be skeptical of this result. It comes down to the figure below: a map of the observed quasars on the sky, where red indicates that the inferred value of α is slightly lower than expected, and blue indicates that it’s slightly higher. As Chad points out, the big red points are mostly circles, while the big blue points are mostly squares. That’s rather significant, because the two shapes represent different telescopes: circles are Keck data, while squares are from the VLT (“Very Large Telescope”). Slightly suspicious that most of the difference comes from data collected by different instruments.

But from a completely separate angle, there is also good reason for theorists to be skeptical, which is what I wanted to talk about. Theoretical considerations will always be trumped by rock-solid data, but when the data are less firm, it makes sense to take account of what we already think we know about how physics works.
The crucial idea here is the notion of a scalar field. That’s just fancy physics-speak for a quantity which takes on a unique numerical value at every point in spacetime. In quantum field theory, scalar fields lead to spinless particles; the Higgs field is a standard example. (Other particles, such as electrons and photons, arise from more complicated geometric objects — spinors and vectors, respectively.)
The fine structure constant is a scalar field. We don’t usually think of it that way, since we usually reserve the term “field” for something that actually varies from place to place rather than remaining constant, but strictly speaking it’s absolutely true. So, while it would be an amazing and Nobel-worthy result to show that the fine structure constant were varying, it wouldn’t be hard to fit it into the known structure of quantum field theory; you just take a scalar field that is traditionally thought of as constant and allow it to vary from place to place and time to time.
That’s not the whole story, of course, When a field varies from point to point, those variations carry energy. Think of pulling a spring, or twisting a piece of metal. For a scalar field, there are three important contributions to the energy: kinetic energy from the field varying in time, gradient energy from the field varying in space, and potential energy associated with the value of the field at every point, unrelated to how it is changing.
For the fine structure constant, the observations imply that it changes by only a very tiny bit from one end of the universe to the other. So we really wouldn’t expect the gradient energy to be very large, and there’s correspondingly no reason to expect the kinetic energy to matter much.
The potential energy is a different matter. The potential is similar to the familiar example of a ball rolling in a hill; how steep the potential is near its minimum is related to the mass of the field. For most scalar fields, like the Higgs field, the potential is extremely steep; this means that if you displace the field from the minimum of its potential by just a bit, it will tend to immediately roll back down.

A priori, we don’t know ahead of time what the potential should look like; specifying it is part of defining the theory. But quantum field theory gives us clues. At heart, the world is quantum, not classical; the “value” of the scalar field is actually the expectation value of a quantum operator. And such an operator gets contributions from the intrinsic vibrations of all the other fields that it couples to — in this case, every kind of charged particle in the universe. What we actually observe is not the “bare” form of the potential, but the renormalized value, which takes into account the accumulated effects of various forms of virtual particles popping in and out of the quantum vacuum.
The basic effect of renormalization on a scalar field potential is easy to summarize: it makes the mass large. So, if you didn’t know any better, you would expect the potential to be as steep as it could possibly be — probably up near the Planck scale. The Higgs boson probably has a mass of order a hundred times the mass of a proton, which sounds large — but it’s actually a big mystery why it isn’t enormously larger. That’s the hierarchy problem of particle physics.
So what about our friend the fine structure constant? Well, if these observations are correct, the field would have to have an extremely tiny mass — otherwise it wouldn’t vary smoothly over the universe, it would just slosh harmlessly around the bottom of its potential. Plugging in numbers, we find that the mass has to be something like 10-42 GeV or less, where 1 GeV is the mass of the proton. In other words: extremely, mind-bogglingly small.
But there’s no known reason for the mass of the scalar field underlying the fine structure constant to be anywhere near that small. This was established in some detail by Banks, Dine, and Douglas. They affirmed our intuition, that a tiny change in the fine structure constant should be associated with a huge change in potential energy.
Now, there are loopholes — there are always loopholes. In this case, you could possibly prevent those quantum fluctuations from renormalizing your scalar-field potential simply by shielding the field from interactions with other fields. That is, you can impose a symmetry that forbids the field from coupling to other forms of matter, or only lets it couple in certain very precise ways; then you could at least imagine keeping the mass small. That’s essentially the strategy behind the supersymmetric solution to the hierarchy problem.
Problem is, that route is a complete failure when we turn to the fine structure constant, for a very basic reason: we can’t prevent it from coupling to other fields, it’s the parameter that governs the strength of electromagnetism! So like it or not, it will couple to the electromagnetic field and all charged particles in nature. I talked about this in one of my own papers from a few years ago. I was thinking about time-dependent scalars, not spatially-varying ones, but the principles are precisely the same.
That’s why theorists are skeptical of this claimed result. Not that it’s impossible; if the data stand up, it will present a serious challenge to our theoretical prejudices, but that will doubtless goad theorists into being more clever than usual in trying to explain it. Rather, the point is that we have good reasons to suspect that the fine structure constant really is constant; it’s not just a fifty-fifty kind of choice. And given those good reasons, we need really good data to change our minds. That’s not what we have yet — but what we have is certainly more than enough motivation to keep searching.

... Read more »

J. K. Webb, J. A. King, M. T. Murphy, V. V. Flambaum, R. F. Carswell, & M. B. Bainbridge. (2010) Evidence for spatial varia. arXiv. arXiv: 1008.3907v1

  • October 18, 2010
  • 11:39 AM

Seeking Depression Information on the Internet

by William Yates, M.D. in Brain Posts

The internet has grown as a source of health information for both clinicians and their patients.  Patients with mental disorders may be particularly drawn to using the internet for information due to the stigma associated with these disorders.  This makes it important for health educators to understand the demographic pattern of searches for health information including depression and other mental disorders.  A recent research study of those seeking information about depression provides some insight into the volume and pattern of web searches for "depression".  Fu et al conducted an interesting study that examined the number and pattern of internet searches for depression.  The authors used the following design in their study:Query for all AOL users web searches between March and May 2006Keyword depression with exclusion of obvious confounders, i.e. "great depression"Limited to U.S. AOL usersReview of database of 21 million web queries.The key results from their study included:3 of every 1000 internet searches sought depression-related information1.16 million search for "depression" estimated per month in the U.S.The most common search areas related to depression were 1. general information 28%, 2. identification/managment 18%, 3. pharmaceutical company depression website 11%, 4. depression-related psychiatric comorbidities, i.e. anxiety disorder or bipolar disorder 7%, 5. female and pregnancy-related depression 5%, 6. teen depression 5%, 7. suicide 0.6%.This study probably underestimates the volume of internet searches related to depression as some individual likely type in the name of a depression drug or other more specific information in their query.The authors note the volume of public searches for depression should stimulate high-quality education for the disorder.  Health educators with high-quality, evidence-based information should also work to keep their information at the top of search engine queries.  There is a significant amount of misinformation about depression and mental disorders on the internet.  There needs to be an effort to make sure individuals searching "depression" get to sites that provide them the information they need to help them make good decisions about their symptoms and disorders. Here are some of the web sites that I feel provide high-quality evidence-based information for the general public:National Institute of Mental HealthMayo Clinic WebMDGoogle HealthDrugs.comNational Association of Cognitive-Behavioral TherapistsIf you have personal experience with sites that you would like to recommend, feel free to post your recommendations in the comments section.Pricky Pear from Enchanted Rock State Natural Area in Texas courtesy of Yates Photography.Fu KW, Wong PW, & Yip PS (2010). What do internet users seek to know about depression from web searches? A descriptive study of 21 million web queries. The Journal of clinical psychiatry, 71 (9), 1246-7 PMID: 20923627... Read more »

  • October 18, 2010
  • 11:33 AM

Pouches, pockets and sacs in the heads, necks and chests of mammals, part III: baleen whales

by Darren Naish in Tetrapod Zoology

Time to continue in the Tet Zoo series on laryngeal diverticula (and other pouches, pockets and sacs). This time, we look at baleen whales, or mysticetes. Like the primates we looked at previously, mysticetes have enlarged laryngeal ventricles* that (mostly) meet along the ventral midline of the throat and form a single large laryngeal pouch or sac. The presence of a raphe along the sac's ventral midline seems to mark the line of fusion between the two ancestral, bilateral sacs. It's probably understandable that few of us are aware of the presence of inflatable laryngeal sacs in mysticetes, but people have known about the existence of these structures for a long time: pioneering scientist and surgeon John Hunter, for example, wrote about their presence in Northern/Common minke whales Balaenoptera acutorostrata in 1787, and they've frequently been remarked on in the cetacean anatomical literature [adjacent cartoon from Desray Reeb's 1997 thesis]. Read the rest of this post... | Read the comments on this post...... Read more »

Mercado E 3rd, Schneider JN, Pack AA, & Herman LM. (2010) Sound production by singing humpback whales. The Journal of the Acoustical Society of America, 127(4), 2678-91. PMID: 20370048  

  • October 18, 2010
  • 11:30 AM

Ed Tronick and the "Still Face Experiment"

by Jason Goldman in The Thoughtful Animal

In 1975, Edward Tronick and colleagues first presented the "still face experiment" to colleagues at the biennial meeting of the Society for Research in Child Development. He described a phenomenon in which an infant, after three minutes of "interaction" with a non-responsive expressionless mother, "rapidly sobers and grows wary. He makes repeated attempts to get the interaction into its usual reciprocal pattern. When these attempts fail, the infant withdraws [and] orients his face and body away from his mother with a withdrawn, hopeless facial expression." It remains one of the most replicated findings in developmental psychology.

Once the phenomenon had been thoroughly tested and replicated, it became a standard method for testing hypotheses about person perception, communication differences as a result of gender or cultural differences, individual differences in attachment style, and the effects of maternal depression on infants. The still-face experiment has also been used to investigate cross-cultural differences, deaf infants, infants with Down syndrome, cocaine-exposed infants, autistic children, and children of parents with various psychopathologies, especially depression.

Why has this experiment, first published in the mid-1970s, become so important?
Read the rest of this post... | Read the comments on this post...... Read more »

  • October 18, 2010
  • 10:12 AM

Florida Panthers - Revived, with a Texan Twist

by Laura Klappenbach in About Animals / Wildlife

Florida panthers are healthier and fitter than they were fifteen years ago. They have higher genetic diversity, better immunity to disease, and fewer genetic abnormalities. They suffer fewer heart defects, enjoy higher fertility and are better able to climb trees. This is wonderful news for a population of panthers that was recently on the brink of extinction.

Like most populations of large carnivores, panther populations are divided between habitat islands and isolated in protected areas such as parks and reserves. Outside these protected lands, panthers face threats such as hunting, habitat destruction and lack of prey. As a result, there is little or no migration between the isolated sub-populations. When panther numbers in any one of the various habitat islands begins to dwindle, inbreeding becomes a concern. This was the case with the Florida panthers.

In the early 1990s, only 20 to 25 adult panthers remained in Florida. The genetic diversity of the population was very low and as a result the panthers suffered a variety of genetic defects and diseases. So in 1995, conservationists intervened. They moved eight female panthers from the Texas population to Florida. They hoped that such a transfer would inject much needed genetic diversity into the ailing Florida panther population.

Read Full PostFlorida Panthers - Revived, with a Texan Twist originally appeared on Animals / Wildlife on Monday, October 18th, 2010 at 14:12:26.Permalink | Comment | Email this... Read more »

Johnson, W., Onorato, D., Roelke, M., Land, E., Cunningham, M., Belden, R., McBride, R., Jansen, D., Lotz, M., Shindle, D.... (2010) Genetic Restoration of the Florida Panther. Science, 329(5999), 1641-1645. DOI: 10.1126/science.1192891  

Packer, C. (2010) A Bit of Texas in Florida. Science, 329(5999), 1606-1607. DOI: 10.1126/science.1196738  

  • October 18, 2010
  • 10:04 AM

Two DonorsChoose projects you must support: Girls are good at math, and Technology tools while pregnant

by Kate Clancy in Context & Variation

A plea to fund DonorsChoose projects that highlights research on sexism in mathematics instruction.... Read more »

Alessandri SM, & Lewis M. (1993) Parental evaluation and its relation to shame and pride in young children. Sex Roles, 335-343. info:/

Fennema, E., Peterson, P., Carpenter, T., & Lubinski, C. (1990) Teachers attributions and beliefs about girls, boys, and mathematics. Educational Studies in Mathematics, 21(1), 55-69. DOI: 10.1007/BF00311015  

  • October 18, 2010
  • 09:49 AM

Alienated Youth More Likely to Lash Out

by APS Daily Observations in Daily Observations

Being rejected by their peers hurts all kids, but they vary in the way they react. Some kids deal with rejection by lashing out, which, taken to the extreme, can ... Read more »

Reijntjes, A., Thomaes, S., Bushman, B.J., Boelen, P.A., de Castro, B.O., & Telch, M.J. (2010) The outcast-lash-out effect in youth: alienation increases aggression following peer rejection. Psychological science : a journal of the Association for Psychological Science/ APS. PMID: 20739674  

  • October 18, 2010
  • 09:47 AM

Fifty percent (50%) of teens have experienced a psychiatric condition by their 18th birthday

by Nestor Lopez-Duran PhD in Child-Psych

Monday’s BRIEFS: Quick musings in child related research. Psychiatric disorders in children and adolescents I: Prevalence and sex differences Today is the first of a series of Brief posts about the results of the latest National Comorbidity Survey (NCS). The NCS is a large nationally representative study of over 10,000 adolescents aged 13 to 18. [...]... Read more »

Merikangas KR, He JP, Burstein M, Swanson SA, Avenevoli S, Cui L, Benjet C, Georgiades K, & Swendsen J. (2010) Lifetime prevalence of mental disorders in U.S. adolescents: results from the National Comorbidity Survey Replication--Adolescent Supplement (NCS-A). Journal of the American Academy of Child and Adolescent Psychiatry, 49(10), 980-9. PMID: 20855043  

  • October 18, 2010
  • 09:46 AM

Tyrannosaurus the Cannibal

by Brian Switek in Dinosaur Tracking

For a Tyrannosaurus rex, there was nothing more dangerous than another Tyrannosaurus rex. From a relatively young age these dinosaurs tussled by biting each other on the face—possibly spreading parasitic microorganisms as they did so—and a few fossil scraps have suggested that some tyrannosaurs may have killed or eaten members of their own kind. This [...]... Read more »

Longrich, N., Horner, J., Erickson, G., & Currie, P. (2010) Cannibalism in Tyrannosaurus rex. PLoS ONE, 5(10). DOI: 10.1371/journal.pone.0013419  

  • October 18, 2010
  • 09:40 AM

Is that my hand? Because it certainly feels like it!

by Psychology 379 bloggers in Cognition & the Arts

... Read more »

  • October 18, 2010
  • 09:21 AM

Colour my world

by Kevin Mitchell in Wiring the Brain

Colour does not exist. Not out in the world at any rate. All that exists in the world is a smooth continuum of light of different wavelengths. Colour is a construction of our brains. A lot is known about how the brain does this, beginning with complicated circuits in the retina itself. Thanks to a new paper from Greg Field and colleagues we now have an even more detailed picture of how retinal circuits are wired to enable light to be categorized into different colours. This study illustrates a dramatic and fundamental principle of brain wiring – namely that cells that fire together, wire together. Colour discrimination begins with the absorption of light of different wavelengths. This is accomplished by photopigment proteins, called opsins, which are expressed in cone photoreceptor cells in the retina. Humans have three opsin genes, which encode proteins that preferentially absorb light of different wavelengths: short (S, in what we perceive as the blue part of the spectrum), medium (M, green) and long (L, red). Each cone expresses only one of these opsin genes and is thus particularly sensitive to light of the corresponding wavelength. However, by itself the response of a single cone cell cannot be used to determine the colour (wavelength) of incoming light. The reason is that each cone is responsive to both the wavelength and the intensity of the light – so an M-cone would respond equally to a dim green light or a strong red light. Colour information only arises by comparing the responses of multiple cone cells. This is accomplished in two distinct channels – one which compares the inputs of L and M cones (the red-green channel) and one which compares the inputs of S cones to the combined inputs of L and M cones (the blue-yellow channel). The latter of these is the original, evolutionarily older system, dating back at least 500 million years. It is found in most mammals, in which there are only two opsin genes – an S opsin and one whose absorbance is midway between L and M. The L/M system evolved much more recently, due to a gene duplication that occurred in the lineage of Old World primates, probably around 40 million years ago. The duplication of the primordial L/M opsin gene allowed the two resultant genes to diverge from each other in sequence, generating proteins with different absorption spectra, which could then be compared. Something similar can actually be achieved even in species with only one copy of the L/M gene. This gene is on the X chromosome, so females will carry two copies of it. Due to the random inactivation of one X chromosome in each cell in females, each cone will express only one of the two copies of this opsin gene. If the two copies differ from each other, encoding proteins with alterations in the amino acid sequence that affect their light absorbance, then what will arise is a set of L cones and a set of M cones. All of this raises an important question – how are the inputs to these different cone cells compared? If the cells which express L and M cones are essentially the same, with the sole difference being that they express different opsin genes, then how is the wiring in the retina set up so that their inputs are distinguished, allowing their subsequent comparison? Cells in the retina are arranged in a series of layers. Cone cells connect, through bipolar and other cells, to retinal ganglion cells, which in turn convey visual information to the brain. Retinal ganglion cells integrate inputs from multiple cones, but in a very specialized way – some cones connect through ON bipolar cells (which are activated by light) and others through OFF bipolar cells (which are inactivated). Typically, one cone in the centre of an array of cells is connected to an ON bipolar cell, while surrounding cones connect to the same retinal ganglion cell target via OFF bipolar cells. The result is that the light signal hitting an array of cones is integrated – if the central cone is an L cell and the surrounding cones are M cells then the retinal ganglion cell will be most strongly activated by red light. This has been known for quite a long time now. What has not been clear is how this system gets wired up during development. S, M and L cones are distributed randomly across the retina. S cones, which are the least frequent, are molecularly distinct from L/M cones in many ways and connect to a dedicated set of S channel bipolar and retinal ganglion cells. The development of the wiring that carries out the comparison between S and L/M cones is thus molecularly specified. This cannot be the case for the comparison between L and M cones, which differ only in the opsin gene they express. The new study by Field and colleagues worked out in breathtaking detail the circuitry of the retina at a cellular level. Their results reveal the beauty and elegance of this circuitry but also resolve an important question relating to how L and M cone cells are wired. Each retinal ganglion cell in the centre of the retina receives ON inputs from a single cone and OFF inputs from the surrounding cones. In the periphery, however, the ON “centre” is composed of up to twelve cones. For the ganglion cell to discriminate colours there must be a bias in how many L or M cone cells wire up to it through the ON and OFF channels. Their results reveal exactly such a bias and further show that it cannot be explained simply by random clumping of L or M cones in the photoreceptor array. What this indicates is that there is some additional mechanism whereby inputs from just one type of cone are strengthened in each of the ON and OFF channels. In effect, the L and M cones are competing for inputs in each channel, presumably through so-called “Hebbian mechanisms” whereby inputs to a cell are strengthened if they fire at the same time and asynchronous inputs are actively weakened. Despite their being no molecular differences between these cone cells, the brain is thus primed to wire them into distinct channels based on their patterns of activity. A remarkable experiment performed a few years ago dramatically illustrates this principle. Mice are naturally dichromatic – they only have two opsin genes (S and L/M). Researchers in Jeremy Nathans’s group replaced one copy of the L/M gene with a version of the human L gene. This meant that female mice could be generated which carried one mouse opsin (L/M) and one human version (L). Cone cells could express one or the other of these genes. The result was astonishing – in visual tests, these mice could clearly distinguish between light of wavelengths which they were previously unable to discriminate. (They could now tell red from green). Despite normally having only two channels, their nervous system was clearly primed to perform this comparison. Amazingly, this may extend to humans as well. The opsin genes in humans can also be polymorphic – each one comes in several different versions. Females who carry one version of, say, the L gene on one X chromosome, and another on the other X chromosome, can effectively have four different channels of absorption: S, M, L and L’. If the retina is primed to compare inputs based on their patterns of activity then one would predict that such females would be tetrachromatic – they should be able to distinguish between more colours than trichromatic individuals (just as trichromats can distinguish more colours than dichromats – people with a mutation in one of the L or M opsin genes, who are red-green colourblind). This increased ability to discriminate colours is, apparently, indeed present in about 50% of females and can be revealed by a very simple test. Consider the picture of the colour spectrum shown below. If you print this out and mark on it with a pencil everywhere there seems to be a clear border between two distinct colours, then what you will find is that most trichromats mark out about 7 colour domains, while tetrachromats mark out between 9-10 (and dichromats about 5). So, where a man may just see “green”, a woman may see chartreuse or olive. Realising that people literally see things differently (and not just colours) could avoid needless argument. (That said, the woman is clearly more right, and it is usually best to concede graciously). ... Read more »

Field GD, Gauthier JL, Sher A, Greschner M, Machado TA, Jepson LH, Shlens J, Gunning DE, Mathieson K, Dabrowski W.... (2010) Functional connectivity in the retina at the resolution of photoreceptors. Nature, 467(7316), 673-7. PMID: 20930838  

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