As a bit of a new theme I am going to each week post up an odd or fascinating quote from a peer reviewed research article. I hope that this will show how awesome science can be and publicise research is not in mainstream consciousness. This week the quote is: “We had no logical explanation for the … Read more... Read more »
Mihailovic Z, Savic S, Damjanjuk I, Stanojevic A, & Milosevic M. (2011) A Case of a Fatal Himalayan Black Bear Attack in the Zoo. Journal of forensic sciences. PMID: 21361947
Foraminifera, Wikimedia Commons
The Pith: The tree if life is nourished by agon, but pruned by the gods. More literally, both interactions between living organisms and the changes in the environment impact the pulsing of speciation and extinction.
No one can be a true “Renaissance Man” today. One has to pick & choose the set of focuses to which one must turn one’s labor to. Life is finite and subject to trade offs. My interest in evolutionary science as a child was trigge........ Read more »
Ezard TH, Aze T, Pearson PN, & Purvis A. (2011) Interplay between changing climate and species' ecology drives macroevolutionary dynamics. Science (New York, N.Y.), 332(6027), 349-51. PMID: 21493859
Today, Sci would like to welcome back to the blog Ambivalent Academic!!! Everyone give her a big hand. We were chatting recently about a cool new paper that came out in Nature on corneal formation in a dish, and she said she'd give it a go on my blog!!! So please welcome Ambivalent Academic and [...]... Read more »
Eiraku M, Takata N, Ishibashi H, Kawada M, Sakakura E, Okuda S, Sekiguchi K, Adachi T, & Sasai Y. (2011) Self-organizing optic-cup morphogenesis in three-dimensional culture. Nature, 472(7341), 51-6. PMID: 21475194
MacLaren, R., Pearson, R., MacNeil, A., Douglas, R., Salt, T., Akimoto, M., Swaroop, A., Sowden, J., & Ali, R. (2006) Retinal repair by transplantation of photoreceptor precursors. Nature, 444(7116), 203-207. DOI: 10.1038/nature05161
The Pith: Over the past 10,000 years a small coterie of farming populations expanded rapidly and replaced hunter-gatherer groups which were once dominant across the landscape. So, the vast majority of the ancestry of modern Europeans can be traced back to farming cultures of the eastern Mediterranean which swept over the west of Eurasia between 10 and 5 thousand years before the before.
Dienekes Pontikos points me to a new paper in PNAS which uses a coalescent model of 400+ mitochondrial DNA l........ Read more »
Gignoux CR, Henn BM, & Mountain JL. (2011) Rapid, global demographic expansions after the origins of agriculture. Proceedings of the National Academy of Sciences of the United States of America, 108(15), 6044-9. PMID: 21444824
Over at the Evolution of Religion Project, Dominic Johnson comments on the first target article which will appear in what promises to be a fantastic new journal, Religion, Brain, and Behavior. Because the first issue has yet to be published, I will have to rely on Johnson’s summary:
Jeff Schloss and Michael Murray have written a [...]... Read more »
perhaps the most notorious New York City bankers, Bernie Madeoff, thewrap.com All people are still dependent on natural resources, but centuries of development complete with urbanization and globalization have removed a large proportion of the world’s population from the production of those natural resources both physically and psychologically. Take, for example, a [...]... Read more »
Mansfield, B. (2010) Is Fish Health Food or Poison? Farmed Fish and the Material Production of Un/Healthy Nature. Antipode. DOI: 10.1111/j.1467-8330.2010.00743.x
Peluso, N., Humphrey, C., & Fortmann, L. (1994) The rock, the beach, and the tidal pool: People and poverty in natural resource-dependent areas. Society , 7(1), 23-38. DOI: 10.1080/08941929409380842
Carter, N., Baland, J., & Platteau, J. (1996) Halting Degradation of Natural Resources: Is There a Role for Rural Communities?. International Affairs (Royal Institute of International Affairs 1944-), 72(4), 821. DOI: 10.2307/2624181
McCarthy, J. (2002) First World political ecology: lessons from the Wise Use movement. Environment and Planning A, 34(7), 1281-1302. DOI: 10.1068/a3526
The last decades of research on human evolution have provided an astounding body of converging evidence for an African origin of the human lineage just under about 200k years ago, with a subsequent migration across the globe starting around 60k years ago until all the main regions of this planet were inhabited by humans at around 15k years ago. Compare this scenario to the creationist story, where humans were shaped by a magic man out of clay about 6k years ago, which means it happened just a........ Read more »
Green, R., Krause, J., Ptak, S., Briggs, A., Ronan, M., Simons, J., Du, L., Egholm, M., Rothberg, J., Paunovic, M.... (2006) Analysis of one million base pairs of Neanderthal DNA. Nature, 444(7117), 330-336. DOI: 10.1038/nature05336
Linz, B., Balloux, F., Moodley, Y., Manica, A., Liu, H., Roumagnac, P., Falush, D., Stamer, C., Prugnolle, F., van der Merwe, S.... (2007) An African origin for the intimate association between humans and Helicobacter pylori. Nature, 445(7130), 915-918. DOI: 10.1038/nature05562
Atkinson, Q. (2011) Phonemic Diversity Supports a Serial Founder Effect Model of Language Expansion from Africa. Science, 332(6027), 346-349. DOI: 10.1126/science.1199295
We had a very nice seminar from Uwe Sauer last week, in celebration of which I thought I would write about one of his papers. Uwe would like to understand how metabolism is controlled, and as a result has done a great deal of work to develop ways to measure metabolic flux. A recent paper [...]... Read more »
Haverkorn van Rijsewijk, B., Nanchen, A., Nallet, S., Kleijn, R., & Sauer, U. (2011) Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli. Molecular Systems Biology. DOI: 10.1038/msb.2011.9
Randall Munroe, the creator of the webcomic XKCD, isn’t going to like this one bit. Fear of attack by Velociraptor is a running theme in the science-themed series—lazy computer programmers should be especially wary—and two separate discoveries announced last week gave those with a phobia of raptors good reason to barricade the doors and windows. [...]... Read more »
Motani, R., & Schmitz, L. (2011) PHYLOGENETIC VERSUS FUNCTIONAL SIGNALS IN THE EVOLUTION OF FORM-FUNCTION RELATIONSHIPS IN TERRESTRIAL VISION. Evolution. DOI: 10.1111/j.1558-5646.2011.01271.x
Schmitz, L., & Motani, R. (2011) Nocturnality in Dinosaurs Inferred from Scleral Ring and Orbit Morphology. Science. DOI: 10.1126/science.1200043
This is turning out to be quite a week for posts on interesting and new things happening in melanoma. Yesterday, we discussed novel mechanisms of resistance to BRAF inhibitors such as PLX4032 and tomorrow we will review new findings associated … Continue reading →
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Wei, X., Walia, V., Lin, J., Teer, J., Prickett, T., Gartner, J., Davis, S., Stemke-Hale, K., Davies, M., Gershenwald, J.... (2011) Exome sequencing identifies GRIN2A as frequently mutated in melanoma. Nature Genetics. DOI: 10.1038/ng.810
Rzeski, W. (2001) From the Cover: Glutamate antagonists limit tumor growth. Proceedings of the National Academy of Sciences, 98(11), 6372-6377. DOI: 10.1073/pnas.091113598
As Maryn McKenna and others have reported, a paper was released on Friday showing a high percentage of drug-resistant Staphylococcus aureus contaminating raw, retail-available meat products. There has been a lot of media coverage of this finding--so what does the study say, and what are its implications? More after the jump.
Read the rest of this post... | Read the comments on this post...... Read more »
Waters, A., Contente-Cuomo, T., Buchhagen, J., Liu, C., Watson, L., Pearce, K., Foster, J., Bowers, J., Driebe, E., Engelthaler, D.... (2011) Multidrug-Resistant Staphylococcus aureus in US Meat and Poultry. Clinical Infectious Diseases. DOI: 10.1093/cid/cir181
Right, I already referred to Atkinson’s paper in a previous post, and much of the work he’s presented is essentially part of a potential PhD project I’m hoping to do. Much of this stems back to last summer, where I mentioned how the phoneme inventory size correlates with certain demographic features, such as population size and population . . . → Read More: The Return of the Phoneme Inventories... Read more »
Atkinson QD. (2011) Phonemic diversity supports a serial founder effect model of language expansion from Africa. Science (New York, N.Y.), 332(6027), 346-9. PMID: 21493858
by in Beaker
Atherosclerotic plaque is the fatty material that builds up on arterial walls, where it can lead to heart disease and stroke. Atherosclerosis is currently treated with dietary changes, angioplasty (which uses a balloon to move the plaque aside) or more invasive procedures. Using drugs to break up these fatty plaques would be an enticing alternative, [...]... Read more »
Hamzah J, Kotamraju VR, Seo JW, Agemy L, Fogal V, Mahakian LM, Peters D, Roth L, Gagnon MK, Ferrara KW.... (2011) Specific penetration and accumulation of a homing peptide within atherosclerotic plaques of apolipoprotein E-deficient mice. Proceedings of the National Academy of Sciences of the United States of America. PMID: 21482787
So according to the authors of a paper in Nature:It suggests rather that language is part of not a specialised module distinct from the rest of cognition, but more part of broad human cognitive skills.The paper is Evolved structure of language shows lineage-specific trends in word-order universals. They found that the various grammatical rules governing the proper order of different words in a sentence changed over time, and crucially that there were no fixed associations between them: no corr........ Read more »
Dunn M, Greenhill SJ, Levinson SC, & Gray RD. (2011) Evolved structure of language shows lineage-specific trends in word-order universals. Nature. PMID: 21490599
Those who know me know my strong dislike of popular accounts of human neuroethology – you know, those articles that report on some study where college student brains were scanned under different emotions and conclusions are drawn (often made up). Even worse are when the actual studies do this. I’m in no position to say [...]... Read more »
Pradel, E., Zhang, Y., Pujol, N., Matsuyama, T., Bargmann, C., & Ewbank, J. (2007) Detection and avoidance of a natural product from the pathogenic bacterium Serratia marcescens by Caenorhabditis elegans. Proceedings of the National Academy of Sciences, 104(7), 2295-2300. DOI: 10.1073/pnas.0610281104
A picture is worth a thousand words, the old saying goes, though what those words are is not always clear.
In November of 2009, National Geographic ran a stunning photograph of a chimpanzee funeral. Sixteen chimpanzees – arrayed behind a wire fence – look on as workers at Cameroon’s Sanaga-Yong Chimpanzee Rescue Center show them the [...]... Read more »
Biro, D., Humle, T., Koops, K., Sousa, C., Hayashi, M., & Matsuzawa, T. (2010) Chimpanzee mothers at Bossou, Guinea carry the mummified remains of their dead infants. Current Biology, 20(8). DOI: 10.1016/j.cub.2010.02.031
Fashing, P., Nguyen, N., Barry, T., Goodale, C., Burke, R., Jones, S., Kerby, J., Lee, L., Nurmi, N., & Venkataraman, V. (2011) Death among geladas (Theropithecus gelada): a broader perspective on mummified infants and primate thanatology. American Journal of Primatology, 73(5), 405-409. DOI: 10.1002/ajp.20902
Warren, Y., & Williamson, E. (2004) Transport of dead infant mountain gorillas by mothers and unrelated females. Zoo Biology, 23(4), 375-378. DOI: 10.1002/zoo.20001
Here we are, so close to the very end. I am pleased and surprised to find that we're now looking at the vesper bats within Vespertilionini - the clade that (in the topology I'm using here: that of Roehrs et al. (2010)) includes the pipistrelles and noctules and their closest relatives. We'll get to those extremely familiar bats soon. As usual, they have a bunch of far less familiar close relatives... or alleged close relatives, or possible close relatives... and it's those bats that we'll be l........ Read more »
Koopman, K. F. (1971) Taxonomic notes on Chalinolobus and Glauconycteris (Chiroptera, Vespertilionidae). American Museum Novitates, 1-10. info:/
...or a storm in a teacup?According to a new paper just out in Nature from the prestigious Salk Institute, schizophrenia may be associated with differences in neural wiring which can be observed in a bunch of cells grown in the lab.The paper is here, and here's an open-access Nature news bit discussing it: Schizophrenia 'in a dish'. It's certainly an incredible piece of biology. They took fibroblasts, a cell found in the skin, from 4 patients with schizophrenia and 6 healthy........ Read more »
Brennand KJ, Simone A, Jou J, Gelboin-Burkhart C, Tran N, Sangar S, Li Y, Mu Y, Chen G, Yu D.... (2011) Modelling schizophrenia using human induced pluripotent stem cells. Nature. PMID: 21490598
Gene networks are popularly used in systems biology to show functional associations among genes within a single genome, taking advantage of available experimental data on intermolecular interactions. Co-evolutionary networks are another way of showing functional associations among genes, in this case using presence/absence patterns of homologous genes across genomes to predict likely interaction partners. A nice example from proteins that I'm interested in are the components of the selenocystein........ Read more »
Xiuwei Zhang, Martin Kupiec, Uri Gophna, & Tamir Tuller. (2011) Analysis of Co-evolving Gene Families Using Mutually Exclusive Orthologous Modules. Genome Biology and Evolution. info:/10.1093/gbe/evr030
The practice of silviculture has been alive and well in the terrestrial ecosystems of our planet for a few centuries. From Latin roots, the term essentially means to grow (culture) the forest (silvi). Such a practice has made both economic and ecological sense in a myriad of biomes on each and every continent. [...]... Read more »
Horoszowski-Fridman, Y., Izhaki, I., & Rinkevich, B. (2011) Engineering of coral reef larval supply through transplantation of nursery-farmed gravid colonies. Journal of Experimental Marine Biology and Ecology. DOI: 10.1016/j.jembe.2011.01.005
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