On the 8th day of Christmas my true love sent to me: 8 streams reversing...
Wind gaps are fossil rivers: water once flowed through these valleys, but now that water has been diverted to flow elsewhere.
Wind Gap in Wheeler Ridge, California. Source (HT to my co-blogger Anne)
Each of the triangles on the drainage map of northern California (from a 2006 paper by Lock et al.) below marks a wind gap that occurs mid-way along a continuous north-south trending channel.
Figure 4 of Lock et al. ........ Read more »
Lock, J., Kelsey, H., Furlong, K., & Woolace, A. (2006) Late Neogene and Quaternary landscape evolution of the northern California Coast Ranges: Evidence for Mendocino triple junction tectonics. Geological Society of America Bulletin, 118(9), 1232. DOI: 10.1130/B25885.1
Research published today... tediously analyzing the genomes from multiple generations of the plant Arabidopsis thaliana, scientists from the Max Planck... Sanger scientists published work in which the rate of mutation in humans was estimated at around...... Read more »
Ossowski, S., Schneeberger, K., Lucas-Lledo, J., Warthmann, N., Clark, R., Shaw, R., Weigel, D., & Lynch, M. (2009) The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana. Science, 327(5961), 92-94. DOI: 10.1126/science.1180677
A short paper in Science offers a new take on camouflage. Usually, we think of camouflage as making an animal hard to detect in the first place. Another possibility, though, is that you can be perfectly visible, but not recognized as the thing you actually are.
Skelhorn and company tested this by taking a couple of different species of caterpillars that seem to mimic twigs (Opisthograptis luteolata is pictured). They exposed chicks (caterpillar predators) to hawthorn branches, which caterpillar........ Read more »
A significant portion of my caseload consists of helping patients recover from tendon disorders. Rotator cuff pathology seems to comprise the greatest percentage of these conditions at our clinic, but there have been no shortage of patellar tendopathy, Achilles tendopathy, and the ubiquitous (read: worn out) diagnosis previously known as tennis elbow.
I was first exposed to [...]... Read more »
Rees, J. (2006) Current concepts in the management of tendon disorders. Rheumatology, 45(5), 508-521. DOI: 10.1093/rheumatology/kel046
How Tasmanian devil facial tumors got their start
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Murchison, E. et al. (2009) The Tasmanian Devil Transcriptome Reveals Schwann Cell Origins of a Clonally Transmissible Cancer. Science. info:/10.1126/science.1180616
"Autism rate in children has doubled, say doctors" ... "Autism 'more common than thought'" ... "Autism in children '10 times higher' than first thought" ... "Autism at a record high" ... "autism is 25 times more common than what researchers thought"... This mess of headlines and claims was generated in response to one autism prevalence study, Baird et al. (2006), published in the Lancet. All 56,946 individuals comprising the targeted population cohort in this study are, as of today, the last day........ Read more »
BAIRD, G., SIMONOFF, E., PICKLES, A., CHANDLER, S., LOUCAS, T., MELDRUM, D., & CHARMAN, T. (2006) Prevalence of disorders of the autism spectrum in a population cohort of children in South Thames: the Special Needs and Autism Project (SNAP). The Lancet, 368(9531), 210-215. DOI: 10.1016/S0140-6736(06)69041-7
Watching adaptation - the process of organisms and populations increasing their fit to the environment - is not easily observed in nature, and when it is, it is often hard to tell what the details of the process are. Crucially, the mutations (and by "mutation" I mean any change to the genome) are mostly unknown, leaving us to guess what kind of genomic changes are responsible for shaping life through evolution.... Read more »
Schoustra SE, Bataillon T, Gifford DR, & Kassen R. (2009) The properties of adaptive walks in evolving populations of fungus. PLoS biology, 7(11). PMID: 19956798
This week in Nature, investigators from Wellcome Trust Sanger Institute published the fourth and fifth complete cancer genomes. Interestingly, both are cancers in which the primary mutagen is known: malignant melanoma (UV light) and small-cell lung cancer (tobacco smoke). This seems to be important, because when I looked at the number of validated somatic coding [...]... Read more »
Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, Greenman CD, Varela I, Lin ML, Ordóñez GR, Bignell GR.... (2009) A comprehensive catalogue of somatic mutations from a human cancer genome. Nature. PMID: 20016485
Pleasance ED, Stephens PJ, O'Meara S, McBride DJ, Meynert A, Jones D, Lin ML, Beare D, Lau KW, Greenman C.... (2009) A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature. PMID: 20016488
Earlier this year, the news of the "discovery" of a caffeine-free species of coffee from the Cameroon created a bit of a stir. This species was actually first collected in 1983, but remained unstudied and not described to science until...
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DAVIS, A., & RAKOTONASOLO, F. (2008) A taxonomic revision of the baracoffea alliance: nine remarkable species from western Madagascar . Botanical Journal of the Linnean Society, 158(3), 355-390. DOI: 10.1111/j.1095-8339.2008.00936.x
A criticism on Hagen's (2008) theory of the evolution of second language acquisition. A new model offers an alternative explanation.... Read more »
L. Kirk Hagen. (2008) The Bilingual Brain: Human Evolution and Second Language Acquisition. Evolutionary Psychology, 43-63. info:/
Review of Kovacs & Mehler (2009), with some data on ABA, AAB and ABB syllable structures from different languages.... Read more »
Kovacs, A., & Mehler, J. (2009) Flexible Learning of Multiple Speech Structures in Bilingual Infants. Science, 325(5940), 611-612. DOI: 10.1126/science.1173947
NOTE: Orac is on semi-vacation this week, trying very hard to recharge his Tarial cells. Actually, although he is at home, he is spending much of his time in his Sanctum Sanctorum (i.e., his home office) working on an R01 for the February submission cycle. Given that the week between Christmas and New Years Day tends to be pretty boring, both from a blogging and blog traffic standpoint, he's scaling back the new, original stuff and mixing in some "best of" reruns, as well as some more recent stu........ Read more »
Berrington de Gonzalez, A., Mahesh, M., Kim, K., Bhargavan, M., Lewis, R., Mettler, F., & Land, C. (2009) Projected Cancer Risks From Computed Tomographic Scans Performed in the United States in 2007. Archives of Internal Medicine_id, 169(22), 2071-2077. http://archinte.ama-assn.org/cgi/doi/10.1001/archinternmed.2009.440
Smith-Bindman, R., Lipson, J., Marcus, R., Kim, K., Mahesh, M., Gould, R., Berrington de Gonzalez, A., & Miglioretti, D. (2009) Radiation Dose Associated With Common Computed Tomography Examinations and the Associated Lifetime Attributable Risk of Cancer. Archives of Internal Medicine, 169(22), 2078-2086. DOI: 10.1001/archinternmed.2009.427
Redberg RF. (2009) Cancer risks and radiation exposure from computed tomographic scans: how can we be sure that the benefits outweigh the risks?. Archives of internal medicine, 169(22), 2049-50. PMID: 20008685
Brenner DJ, & Hall EJ. (2007) Computed tomography--an increasing source of radiation exposure. The New England journal of medicine, 357(22), 2277-84. PMID: 18046031
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Santos, M., & Whitham, T. (2009) Predictors of Ips confusus Outbreaks During a Record Drought in Southwestern USA: Implications for Monitoring and Management. Environmental Management. DOI: 10.1007/s00267-009-9413-6
If a patient with a complicated psychiatric history suffers a traumatic brain injury and then develops new psychological problems, how do you know whether the new problems are related to the head injury or the prior psychiatric diagnoses? This dilemma forms the latest 'complex case' to appear in the journal Personality and Mental Health where it is accompanied by five expert commentaries. The complex case is described by psychiatrist Kathleen Diehl at the University of Michigan. She undertook se........ Read more »
Diehl, K. (2009) Head trauma, dissociation and possible development of multiple personalities. Personality and Mental Health, 3(4), 295-301. DOI: 10.1002/pmh.95
Jinbo Hu (Shanghai Institute of Organic Chemistry) and coworkers have synthesized the Z isomer of monofluoroalkenes in high yield, which will be useful towards designing protein-based drugs that resist degradation within the body. This news feature was written on December 30, 2009.... Read more »
Zhang, W., Huang, W., & Hu, J. (2009) Highly Stereoselective Synthesis of Monofluoroalkenes from alpha-Fluorosulfoximines and Nitrones. Angewandte Chemie International Edition, 48(52), 9858-9861. DOI: 10.1002/anie.200905077
Death elasticity and the estate tax.... Read more »
Kopczuk, W., & Slemrod, J. (2003) Dying to Save Taxes: Evidence from Estate-Tax Returns on the Death Elasticity. Review of Economics and Statistics, 85(2), 256-265. DOI: 10.1162/003465303765299783
Gans, J., & Leigh, A. (2006) Did the Death of Australian Inheritance Taxes Affect Deaths?. Topics in Economic Analysis , 6(1). DOI: 10.2202/1538-0653.1654
I often get questions about bioinformatics, bioinformatics jobs and career paths. Most of the questions reflect a general sense of confusion between creating bioinformatics resources and using them. Bioinformatics is unique in this sense. No one confuses writing a package like Photoshop with being a photographer, yet for some odd reason, people seem to expect this of biologists. In the same respect, even the programmers and database administrators who work in bioinformatics, are unfairly ass........ Read more »
Dudley, J., & Butte, A. (2009) A Quick Guide for Developing Effective Bioinformatics Programming Skills. PLoS Computational Biology, 5(12). DOI: 10.1371/journal.pcbi.1000589
Demand from aquarium enthusiasts may fuel invertebrate fishery collapse
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Rhyne, A., Rotjan, R., Bruckner, A., & Tlusty, M. (2009) Crawling to Collapse: Ecologically Unsound Ornamental Invertebrate Fisheries. PLoS ONE, 4(12). DOI: 10.1371/journal.pone.0008413
While my Christmas post was of the gloomy kind, most blogs I follow had more heart-warming stories. Sociolingo Africa picked up a press release coming out of Orlando, Florida issued by who-I-don’t-know, about new translations of the Christmas story becoming available just in time for this year’s event. According to the press release, the Wycliffe [...]... Read more »
Errington, Joseph. (2008) Linguistics in a colonial world: a story of language, meaning, and power. Blackwell Publishing. info:/
James Hansen (NASA Goddard Institute for Space Studies, New York) and coworkers have determined why glaciers on the Tibetan Plateau are quickly melting, and offer possible solutions for preserving this essential water source for future generations. This news feature was written on December 30, 2009.... Read more »
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