Post List

  • April 15, 2009
  • 04:24 AM

The information flow model for Protein-protein interaction networks

by Abhishek Tiwari in Fisheye Perspective

In a recent article published in PLoS computational biology Missiuro et al. have developed a novel network analysis method which models an interactome network as an electrical circuit, where protein-protein interactions are modeled as resistors and proteins as interconnecting junctions. The resistance of each resistor is inversely proportional to the confidence score of the corresponding interaction or protein interaction probabilities. Method tries to identify proteins central to the transmi........ Read more »

Missiuro, P., Liu, K., Zou, L., Ross, B., Zhao, G., Liu, J., & Ge, H. (2009) Information Flow Analysis of Interactome Networks. PLoS Computational Biology, 5(4). DOI: 10.1371/journal.pcbi.1000350  

  • April 15, 2009
  • 01:47 AM

Is that glass within reach? Ask your parieto-occipital cortex

by Evil Monkey in Neurotopia

So I'm settled down to blogging of an evening, with some chocolate (the leftover Easter candy continues), some wine, and Sci-cat. Sci-cat has a wonderful talent for sitting JUST out of reach, and purring loudly, hoping that you, her servant, will show proper deference and move to pet her. At which point she will move JUST out of reach again, purr invitingly, and do her best to look charming. She can do this for hours. Sci, however, has less patience.

But how do I KNOW that Sci-cat is just o........ Read more »

  • April 14, 2009
  • 10:07 PM

How different could life be under a red dwarf sun?

by Invader Xan in Supernova Condensate

I’ve been mulling over this paper for a few days now. Last week, NASA JPL put out a press release about cool stars having a different mix of life forming chemicals to sun-like stars. The release was immediately picked up by news sites and bloggers alike. With good reason too — the findings could have a lot of implications for future astrobiology searches. With my interest piqued, I thought I’d get hold of a copy of the paper and find out more…... Read more »

I. Pascucci, D. Apai, K. Luhman, Th. Hemming, J. Bouwman, M. R. Meyer, F. Lahuis, A. Natta. (2009) The Different Evolution of Gas and Dust in Disks around Sun-like and Cool Stars. Astrophysical Journal (submitted). DOI:  

  • April 14, 2009
  • 05:57 PM

The problem with studies on the social effects of religion...

by Tom Rees in Epiphenom

One of the many newspaper columns published over the weekend was this one, in The Miami Herald, on the alleged beneficial effects of religion. Most of it was drawn from the work of Mike McCullough, a psychologist at the University of Miami.McCullough's research suggests that religious people of all faiths, by sizable margins, do better in school, live longer, have more satisfying marriages and are generally happier than their nonbelieving peers.Yes well, that's all true enough, but does it justi........ Read more »

  • April 14, 2009
  • 05:48 PM

Neuroscience of Envy and Schadenfreude

by Jake Young in Pure Pedantry

I don't think I am alone in saying that I often feel a little envy and schadenfreude towards my peers. Science is a particularly competitive business with few remunerative rewards, so a lot of my self-worth is tied to comparisons with my peer's successes and failures. I won't deny being envious when someone gets a Science paper. And while seeing the abject failure of my peers isn't high on my list of priorities, I won't deny the small satisfaction that I get when someone who breezed through t........ Read more »

  • April 14, 2009
  • 04:36 PM

Much ado about protein dynamics

by The Curious Wavefunction in The Curious Wavefunction

Let me alert you, in case you haven't noticed, to the latest issue of Science which is a special issue on protein dynamics. There is much of merit here, but this article is especially relevant to drug discovery. It talks about the interaction of small molecules and how it reshapes the energy landscape of protein conformational motion. One of the most useful ways of thinking about small molecule-protein interactions is to visualize a protein that fluctuates between several conformational states w........ Read more »

  • April 14, 2009
  • 03:52 PM

What it will take to cut global warming in half

by James Hrynyshyn in Class M

A new paper to be published next week in Geophysical Review Letters (which really needs a better name) lays out what kind of effort would be required to reduce the impacts of climate change by half. Actually, what it does is conclude that if we reign in our fossil-fuel emissions by 70%, temperature rise and a few other consequences will be roughly half of what they'd be in the absence of any mitigating effort. But since both targets are arbitrary, it doesn't really matter which way you approach ........ Read more »

Warren Washington, et al. (209) How much climate change can be avoided by mitigation. Geophysical Research Letters.

  • April 14, 2009
  • 12:00 PM

Is what you drink more important than what you eat?

by Christie Wilcox in Nutrition Wonderland

Most of us feel like we could be a little more toned or lose those couple of extra pounds of belly fat. Yet we diet, eat less, and still seem to have the same problems. Sure, part of the problem is our nit-picky view of our bodies, but there might just be another problem, too. We’re watching what we eat, not what we drink.

Scientists from the Johns Hopkins Bloomberg School of Public Health in Baltimore, MD have found that the liquid calories we drink, in everything from sports drinks to........ Read more »

Chen, L., Appel, L., Loria, C., Lin, P., Champagne, C., Elmer, P., Ard, J., Mitchell, D., Batch, B., Svetkey, L.... (2009) Reduction in consumption of sugar-sweetened beverages is associated with weight loss: the PREMIER trial. American Journal of Clinical Nutrition, 89(5), 1299-1306. DOI: 10.3945/ajcn.2008.27240  

  • April 14, 2009
  • 11:00 AM

The slow death of inbreeding

by thegiantsquid in Research i find awesome

As a caveat, I do not profess to be a geneticist, although this study is straightforward enough that I feel like I understand it well enough to explain it.This one, from this month's PLOS Genetics, is interesting, not necessarily for its methodology, but more for some of the conclusions that can be drawn from its results. What the researchers did is take two groups of heterogenous, American people, aged 19-99, performed genome-wide analyses, and quantified the degree of autozygosity within each........ Read more »

Nalls, M., Simon-Sanchez, J., Gibbs, J., Paisan-Ruiz, C., Bras, J., Tanaka, T., Matarin, M., Scholz, S., Weitz, C., Harris, T.... (2009) Measures of Autozygosity in Decline: Globalization, Urbanization, and Its Implications for Medical Genetics. PLoS Genetics, 5(3). DOI: 10.1371/journal.pgen.1000415  

  • April 14, 2009
  • 09:53 AM

Children with Psychopathic traits may have difficulty hearing the victim

by Nestor L. Lopez-Duran PhD in Child-Psych

A study examining the perception of victim distress signals among children with psychopathic traits indicates that these children have the capacity to identify and respond to the victim's distress, but these children may have their "distress radar" turned to "low". A review of: van Baardewijk, Y., Stegge, H., Bushman, B., & Vermeiren, R. (2009). Psychopathic traits, victim distress and aggression

Read the full post at

Read the full post at

Read the full........ Read more »

van Baardewijk, Y., Stegge, H., Bushman, B., & Vermeiren, R. (2009) Psychopathic traits, victim distress and aggression in children. Journal of Child Psychology and Psychiatry. DOI: 10.1111/j.1469-7610.2008.02023.x  

  • April 14, 2009
  • 09:32 AM

Free Will and the Philosophy of Science

by Shaheen Lakhan in Brain Blogger

For many years the discussion over the existence of free will was limited to philosophers and theologians. Scientists started talking about free will once science started separating as a discipline from philosophy. However, it wasn’t until the rise of functional neuroimaging that some neuroscientists started studying if the brain and deterministic brain processes could explain [...]... Read more »

Soon, C., Brass, M., Heinze, H., & Haynes, J. (2008) Unconscious determinants of free decisions in the human brain. Nature Neuroscience, 11(5), 543-545. DOI: 10.1038/nn.2112  

  • April 14, 2009
  • 09:22 AM

Finding Nemo by DNA parentage analysis

by Peter Etnoyer in Deep Sea News

Since the first observations of transoceanic dispersal in marine snails (Scheltema 1971), long distance transport for marine animals has been a kind of Holy Grail for marine conservation science. Marine protected area (MPA) networks make sense to coral lovers, for instance, because most coral reef fish have pelagic larval durations exceeding 30 days. Lobster larvae [...]... Read more »

Planes, S., Jones, G., & Thorrold, S. (2009) Larval dispersal connects fish populations in a network of marine protected areas. Proceedings of the National Academy of Sciences, 106(14), 5693-5697. DOI: 10.1073/pnas.0808007106  

  • April 14, 2009
  • 08:57 AM

Design and engineering of an O2 transport protein

by Nir London in Macromolecular Modeling Blog

In a recent Nature paper Koder & Anderson et al. describe the procedure for creating an O2 transport protein from first principals. The paper is somewhat technical and may appeal to the biochemists amongst our readers, here we present the main ideas, findings and conclusions.... Read more »

Koder, R., Anderson, J., Solomon, L., Reddy, K., Moser, C., & Dutton, P. (2009) Design and engineering of an O2 transport protein. Nature, 458(7236), 305-309. DOI: 10.1038/nature07841  

  • April 14, 2009
  • 07:29 AM

Tumor immunity: The Goldilocks approach

by iayork in Mystery Rays from Outer Space

We know that the immune system can destroy tumors. We also know, unfortunately, that by the time we see a tumor, immunity probably won’t destroy the tumor. There are lots of reasons for that. One is that tumors are essentially part of the normal body, so it’s normal for the immune system [...]... Read more »

Rizzuto, G., Merghoub, T., Hirschhorn-Cymerman, D., Liu, C., Lesokhin, A., Sahawneh, D., Zhong, H., Panageas, K., Perales, M., Altan-Bonnet, G.... (2009) Self-antigen-specific CD8 T cell precursor frequency determines the quality of the antitumor immune response. Journal of Experimental Medicine, 206(4), 849-866. DOI: 10.1084/jem.20081382  

  • April 14, 2009
  • 06:30 AM

The waterfall illusion can be transferred between vision and touch

by Mo in Neurophilosophy

If you look at a waterfall for about 30 seconds, and then shift your gaze to a nearby stationary object, such as a rock or a tree, that object will seem to drift slowly upwards. This well known optical illusion demonstrates a phenomenon called the motion after-effect, which is thought to occur as a result of adaptation - the brain compensates for movement in one direction, causing us to momentarily perceive a stationary objects to be moving in the other.

Although illusory motion can also be ind........ Read more »

  • April 14, 2009
  • 05:00 AM

When and how should new therapies become routine clinical practice?

by Bronwyn Thompson in Healthskills: Skills for Healthy Living

Bo and Herbert argue that the current way that new therapies become integrated into our daily clinical work is ‘far from optimal because innovative therapies still become accepted practice on the basis of laboratory research alone.’ I agree. Worse still, old therapies that have little evidence to support them continue to be used - even in the face of clinical studies demonstrating that they have no greater effect than placebo.... Read more »

  • April 14, 2009
  • 02:52 AM

Male Chauvinist Chimps or the Meat Market of Public Opinion?

by Eric Michael Johnson in The Primate Diaries

A new study in the journal PLoS One, by Cristina Gomes and Christophe Boesch of the Max Planck Institute for Evolutionary Anthropology, finally answered a question that has intrigued primatologists for nearly two decades. Do female chimpanzees preferentially mate with males who share their hunting gains with them? This hypothesis was first suggested in 1994 by Craig Stanford and Jane Goodall when they found that the best predictor for whether males would engage in a hunt or not was the presence ........ Read more »

  • April 14, 2009
  • 01:07 AM

Stefan and the Polar Ice Caps

by Arunn in nOnoScience (a.k.a. Unruled Notebook)

Melting of polar ice caps is a topic of current interest due to global warming and its impact. But not long back in human history, in times of lesser pollution and implication, the inverse problem of solidification or growth of polar ice was of interest. During mid nineteenth century Arctic expeditions to study polar ice [...]... Read more »

  • April 14, 2009
  • 12:00 AM

We like to exploit the luck of others

by Christian Jarrett in BPS Research Digest

Psychologists have documented the many irrational ways we think about luck, from the fact we prefer to make our own choice in gambling games (thus increasing our sense of control) to our belief in lucky runs or hot numbers. Now Michael Wohl and Michael Enzle have extended this research by showing that we are prepared to hand over control to others if we believe they are likely to be luckier than we are. Wohl and Enzle call this "illusion of control by proxy".Across three experiments, university ........ Read more »

  • April 13, 2009
  • 10:00 PM

Drugs disrupt DHFR dynamics

by Michael Clarkson in Conformational Flux

One of the most-studied cases of the relationship between dynamics and catalysis is the bacterial dihydrofolate reductase (DHFR). DHFR catalyzes the reduction of dihydrofolate to tetrahydrofolate while oxidizing the cofactor nicotinamide adenine dinucleotide phosphate (NADPH). As part of this catalytic process, a region of the protein called the "Met 20 loop" switches from a "closed" state that shields the active site from solvent to an "occluded" state that separates the substrate from the cofa........ Read more »

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