Sue Storm tries hard to use her favorite force field to counter the 1 kcal/mol barrierEvery once in a while there is a study asking what method X (X = docking, free energy calculations, molecular dynamics, force fields etc.) is good for. Such studies can be useful to take stock of a particular paradigm. So the question that Jonathan Goodman and his group ask in this paper is "Are force fields good for reproducing non-bonded interactions, especially hydrogen bonding, pi-stacking and dispersion?"......... Read more »
Paton, R., & Goodman, J. (2009) Hydrogen Bonding and π-Stacking: How Reliable are Force Fields? A Critical Evaluation of Force Field Descriptions of Nonbonded Interactions. Journal of Chemical Information and Modeling, 49(4), 944-955. DOI: 10.1021/ci900009f
This is a brief report and some links from the second day of Network Applications and Tools in Biology (NETTAB 2009) in Catania, Sicily. There were two keynotes on the RNA WikiProject  by Alex Bateman and myExperiment  (by me) as as well as presentations by (I think but I wasn’t concentrating enough) Dietlind [...]... Read more »
Daub, J., Gardner, P., Tate, J., Ramskold, D., Manske, M., Scott, W., Weinberg, Z., Griffiths-Jones, S., & Bateman, A. (2008) The RNA WikiProject: Community annotation of RNA families. RNA, 14(12), 2462-2464. DOI: 10.1261/rna.1200508
Gardner, P., Daub, J., Tate, J., Nawrocki, E., Kolbe, D., Lindgreen, S., Wilkinson, A., Finn, R., Griffiths-Jones, S., Eddy, S.... (2009) Rfam: updates to the RNA families database. Nucleic Acids Research, 37(Database). DOI: 10.1093/nar/gkn766
Reyes-Palomares, A., Montanez, R., Real-Chicharro, A., Chniber, O., Kerzazi, A., Navas-Delgado, I., Medina, M., Aldana-Montes, J., & Sanchez-Jimenez, F. (2009) Systems biology metabolic modeling assistant: an ontology-based tool for the integration of metabolic data in kinetic modeling. Bioinformatics, 25(6), 834-835. DOI: 10.1093/bioinformatics/btp061
How many ways are there for defining vulnerability and criticality, really? Traditionally, risk matrixes have a likelihood/impact approach, but not always. Yesterday, I was examining a criticality/vulnerability matrix. Today, I will take a closer look at a criticality/preparedness matrix with a third susceptibility dimension added to it, as presented in the New Zealand research project [...]... Read more »
Erica Seville, David Brunsdon, Andre Dantas, Jason Le Masurier, Suzanne Wilkinson, & John Vargo. (2008) Organisational resilience: Researching the reality of New Zealand organisations. Journal of Business Continuity , 2(3), 258-266. DOI: henrystewart.metapress.com/index/Q5W8L24Q93842U01.pdf
New evidence that the closest living relative of humans is the orangutan, and not the chimpanzee.... Read more »
John R. Grehan1 and Jeffrey H. Schwartz. (2009) Evolution of the second orangutan: phylogeny and biogeography of hominid origins. Journal of Biogeography. DOI: http://www.blackwellpublishing.com/pdf/jbi_2141.pdf
What are the causes of homosexual behavior in animals? Contrary to what most people probably think, homosexual behavior is not just common in animals, it is catholic.
A new paper in TREE has gotten a lot of press (most papers on sex do, I suspect): Same-sex sexual behavior and evolution, by Bailey and Zuk at UC Riverside.... Read more »
Nathan W. Bailey, Marlene Zuk. (2009) Same-sex sexual behavior and evolution. Trends in Ecology . DOI: http://www.sciencedirect.com/science/article/B6VJ1-4WJ8FG7-1/2/a146e8248e9ca604894abfd9f0c3aabd
To call Jerusalem a disputed location would be an under-statement. The Temple Mount in that city might be the most hotly contested piece of real estate on the planet, sacred as it is to the 3 major western religions: Judaism, Christianity, and Islam. Archaeologists believe that there has been a city on the site of Jerusalem since about 2600 BCE, meaning that for nearly 5000 years, various groups of people have fought over the landscape: Judeans, Israelites, Assyrians, Babylonians, Persians, Gre........ Read more »
Greenberg, R. (2009) "Towards an Inclusive Archaeology in Jerusalem: The Case of Silwan/The City of David.". Public Archaeology, 8(1), 35-50. DOI: 10.1179/175355309X402745
[Originally posted in April 2007]
One "trick" dieters often use is to put their food on a smaller plate. The idea is to fool yourself into thinking you're eating more food than you really are. But doesn't our stomach tell us how full we are?
Actually, it doesn't. Brian Wansink has devoted his career to studying how perception of food intake relates to actual eating behavior. Together with James Painter and Jill North, he's come up with a dramatic demonstration of how wrong our stomachs can be......... Read more »
Wansink, B., Painter, J.E., & North, J. (2005) Bottomless Bowls: Why Visual Cues of Portion Size May Influence Intake. Obesity Research, 13(1), 93-100.
News from my Newcastle University published today reveals that cooking carrots whole and then chopping them before serving is better for your health than slicing and dicing before you boil.
Apparently, less of the “anticancer” compound falcarinol leaches out of the carrots and into the cooking water if carrots are boiled whole. Of course, the truly [...]... Read more »
Christensen, L., Vach, W., Ritskes-Hoitinga, J., & Brandt, K. (2005) Inhibitory Effects of Feeding with Carrots or (−)-Falcarinol on Development of Azoxymethane-Induced Preneoplastic Lesions in the Rat Colon. Journal of Agricultural and Food Chemistry, 53(5), 1823-1827. DOI: 10.1021/jf048519s
Geoengineering is the idea that humans can slow, stop or reverse the effects of climate change by altering the composition of Earth’s atmosphere and biosphere. While controversial, these methods, including reducing sun exposure by injecting aerosols into the atmosphere or using giant mirrors to reflect the sun’s rays, were identified as a high-priority area for [...]... Read more »
Matthews, H. D., L. Cao, & K. Caldeira. (2009) Sensitivity of ocean acidification to geoengineered climate stabilization. Geophysical Research Letters. DOI: http://www.agu.org/pubs/crossref/2009/2009GL037488.shtml
Photo by Marina KomolovaOne topic that never fails to generate a lively discussion is the relationship between obesity and personal responsibility. For example, in response to a post on psychological exams for bariatric surgery patients, one anonymous reader commented that: I don't have a gym membership. I'm not even all that active. I live in a bad neighbourhood and i'm floating right around the Canadian poverty line. I'm not obese. When I see a little extra belly buil........ Read more »
I was quite excited recently to receive an alert about this new paper by Nomaki et al. The authors ‘labelled’ phytoplankton – microscopic algae – with the carbon stable isotope 13C, which is easily done by adding amounts of the isotope to a batch of growing algae who will happily incorporate it into (among other things) the fatty acids they contain. The tracer can then later be detected in the algae and any organism that eats them. Nomaki et al. then fed these labelled al........ Read more »
Nomaki, H., Ohkouchi, N., Heinz, P., Suga, H., Chikaraishi, Y., Ogawa, N., Matsumoto, K., & Kitazato, H. (2009) Degradation of algal lipids by deep-sea benthic foraminifera: An in situ tracer experiment. Deep Sea Research Part I: Oceanographic Research Papers. DOI: 10.1016/j.dsr.2009.04.013
I'm rather interested in "urban ecology", and by this, I usually mean the flora, fauna, and fungi that manages to exist in urban spaces in spite of, or better yet, in concert with Homo sapiens. I'm particularly interested in the behavioural adaptations of animals (e.g. foxes learning to look before they cross the street) and the exploitation of anthropogenic resources, like tasty, tasty garbage, or the sheltered, warm nesting space that can be found in lit up Wal-Mart Signs.Figure 1: Ferns growi........ Read more »
DUNN, R., GAVIN, M., SANCHEZ, M., & SOLOMON, J. (2006) The Pigeon Paradox: Dependence of Global Conservation on Urban Nature. Conservation Biology, 20(6), 1814-1816. DOI: 10.1111/j.1523-1739.2006.00533.x
There is a surprising amount of truth in the old adage that “the eyes are the window to the soul.” We possess an innate ability to understand that the focus of someone else’s vision is the object of her attention. This ability is an important part of autism researcher Simon Baron-Cohen’s model for [...]... Read more »
Shepherd, S., Klein, J., Deaner, R., & Platt, M. (2009) Mirroring of attention by neurons in macaque parietal cortex. Proceedings of the National Academy of Sciences, 106(23), 9489-9494. DOI: 10.1073/pnas.0900419106
by Nestor Lopez-Duran PhD in Child-Psych
The Journal of Autism and Developmental Disorders recently published a study examining the effectiveness of a Portable Digital Assistant (PDA) as an aid device for adolescents with autism spectrum disorders. I was surprised to read that only a couple of studies have been conducted examining the potential utility of PDAs in autism. The portability of [...]... Read more »
Mechling, L., Gast, D., & Seid, N. (2009) Using a Personal Digital Assistant to Increase Independent Task Completion by Students with Autism Spectrum Disorder. Journal of Autism and Developmental Disorders. DOI: 10.1007/s10803-009-0761-0
It's a far cry from the almond eyes and radiant smiles of poetry, but according to psychology research, beauty lies, with some sterility, in the averageness and symmetry of a face. That much we know.The trouble is, studies on this topic have tended to create highly average faces by morphing lots of real faces altogether, and in the process they've created faces that are also highly symmetrical. It's a similar tale for investigations of symmetry, where the creation of artificially symmetrical fac........ Read more »
Komori, M., Kawamura, S., & Ishihara, S. (2009) Averageness or symmetry: Which is more important for facial attractiveness?. Acta Psychologica, 131(2), 136-142. DOI: 10.1016/j.actpsy.2009.03.008
Tiger beetles have long enjoyed a popularity that is disproportionate to their diversity, abundance, and economic importance relative to other groups of beetles. This seems as much due to their charismatic behavior – toothy jawed predators in extreme habitats – as it is to their brilliant colors, dazzling designs, and penchant for polytopism. Never before [...]... Read more »
Erwin, T. L. and D. L. Pearson. (2008) A Treatise on the Western Hemisphere Caraboidea (Coleoptera). Their classification, distributions, and ways of life. Volume II (Carabidae-Nebriiformes 2-Cicindelitae). Pensoft Series Faunistica 84., 1-400.
Since the Swine Influenza Media and Blogging Pandemic has died for now, I think I can finally write about ‘flu myself. A quick aside: until I was about 15, I thought that the word Influenza came from the Arabic “Inf-Il-enza” meaning “goat’s nose”, which it is a bit runny, like a dog’s, or like [...]... Read more »
Allen, J., Gardner, S., Vitalis, E., & Slezak, T. (2009) Conserved amino acid markers from past influenza pandemic strains. BMC Microbiology, 9(1), 77. DOI: 10.1186/1471-2180-9-77
Researchers from Myanmar and Thailand have a paper in Field Crops Research describing how they managed to get the prized gene for fragrance into a local rice variety which smelled, well, ordinary.
They started out with Manawthukha, a very well-liked but alas non-fragrant variety from Myanmar, and Basmati, which of course is the most famous of [...]... Read more »
Yi, M., Nwe, K., Vanavichit, A., Chai-arree, W., & Toojinda, T. (2009) Marker assisted backcross breeding to improve cooking quality traits in Myanmar rice cultivar Manawthukha. Field Crops Research. DOI: 10.1016/j.fcr.2009.05.006
We are all descendents of an unbroken line of cell divisions, dating back to the last common ancestor of all life on Earth. At some point, long after our lineage had acquired features like nuclei and mitochondria, a less distant ancestor stumbled on a major innovation: it grew a body, bringing with it the advantages [...]... Read more »
Curran, S., Wu, X., Riedel, C., & Ruvkun, G. (2009) A soma-to-germline transformation in long-lived Caenorhabditis elegans mutants. Nature. DOI: 10.1038/nature08106
by Vincent Racaniello in virology blog
WHO reports that as of 15 June 2009, 76 countries have officially reported 35, 928 cases of influenza A(H1N1) infection, including 163 deaths. These numbers can be used to calculate a case fatality ratio (CFR) of 0.45%. Is this number an accurate indication of the lethality of influenza?
Determining how many people die from influenza is [...]... Read more »
Dushoff, J. (2005) Mortality due to Influenza in the United States--An Annualized Regression Approach Using Multiple-Cause Mortality Data. American Journal of Epidemiology, 163(2), 181-187. DOI: 10.1093/aje/kwj024
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