A large merged double edition of the journal Rejuvenation Research is now online, bringing with it a lot of papers to look through. I thought I'd direct your attention to one of those many papers, as it presents an interesting evolutionary background to the SENS approach to the mitochondrial DNA damage that accumulates with age. Our mitochondria are biological power plants within our cells, the evolved descendants of symbiotic bacterial species. They convert food into ATP, the chemical used as f........ Read more »
Components of the newly-described Fezouata fauna. a, Demosponge Pirania auraeum b, Choiid demosponge c, Annelid worm d, Organism showing possible similarities to halkieriids e, Possible armoured lobopod f, Thelxiope-like arthropod g, Marrellomorph arthropod, probably belonging to the genus Furca h, Skaniid arthropod i, Spinose arthropod appendage
apparatus consisting of six overlapping elements. From Van Roy et al, 2010.
When the Cambrian period comes up in conversation, it is usually in re........ Read more »
I bet you never wondered why the black ghost knifefish hunts at an uncomfortable angle of -30°! Prepare to take a journey on the intersection of animal behaviour, neurobiology and biomechanics!
Suppose you’re one of your animal ancestors, swimming around in one of the warm and shallow Cambrian seas 500 million years ago. You’re a small [...]... Read more »
MacIver, M., Patankar, N., & Shirgaonkar, A. (2010) Energy-Information Trade-Offs between Movement and Sensing. PLoS Computational Biology, 6(5). DOI: 10.1371/journal.pcbi.1000769
Global warming may already be driving lizard populations extinct
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Sinervo, B. et al. (2010) Erosion of lizard diversity by climate change and altered thermal niches. Science. info:/10.1126/science.1184695
Huey, R.B., Losos, J.B., & C. Moritz. (2010) Are lizards toast?. Science. info:/10.1126/science.1190374
“Human beings are now carrying out a large scale geophysical experiment of a kind that could not have happened in the past nor be reproduced in the future. Within a few centuries, we are returning to the atmosphere and oceans the concentrated organic carbon stored in sedimentary rocks over hundreds of millions of years.” - [...]... Read more »
Veron, J. (2008) Mass extinctions and ocean acidification: biological constraints on geological dilemmas. Coral Reefs, 27(3), 459-472. DOI: 10.1007/s00338-008-0381-8
Yesterday, the CBC reported a story of a University of Alberta scientist who managed to raise funds from private donors to test the effects of an unconventional (and unpatented) drug in the fight against cancer (see Potential brain-cancer drug shows promise). The study was recently published in The Journal Science Translational Medicine (see bottom of [...]... Read more »
Michelakis, E., Sutendra, G., Dromparis, P., Webster, L., Haromy, A., Niven, E., Maguire, C., Gammer, T., Mackey, J., Fulton, D.... (2010) Metabolic Modulation of Glioblastoma with Dichloroacetate. Science Translational Medicine, 2(31), 31-31. DOI: 10.1126/scitranslmed.3000677
by Southern Fried Scientist and Bluegrass Blue Crab in Southern Fried Science
Menhaden were the most important fisheries throughout American history. When the first settlers learn to farm corn, it was with menhaden that they fertilized the seeds. When the whaling industry reached its height, it was outweighed by menhaden oil. Menhaden ruled the ocean from the middle of the food chain, they [...]... Read more »
G. Brown Goode. (1880) A History of the Menhaden. Menhaden Fisheries. info:/
When it comes to habitat destruction, startling events like oil spills and deforestation are certain to grab the headlines.
Yet as a new study in the journal Animal Conservation shows, sometimes habitat destruction can be so subtle that it passes under the eyes of all but the most astute scientists.... Read more »
Pike, D., Croak, B., Webb, J., & Shine, R. (2010) Subtle - but easily reversible - anthropogenic disturbance seriously degrades habitat quality for rock-dwelling reptiles. Animal Conservation. DOI: 10.1111/j.1469-1795.2010.00356.x
In a bid to find a solution to the dual crises of climate change and deforestation, the REDD program has emerged as a potential "win-win" conservation idea. However, the question arises whether underlying social and economic preconditions exist in many countries for REDD to be successful...... Read more »
Börner, J., Wunder, S., Wertz-Kanounnikoff, S., Tito, M., Pereira, L., & Nascimento, N. (2010) Direct conservation payments in the Brazilian Amazon: Scope and equity implications. Ecological Economics, 69(6), 1272-1282. DOI: 10.1016/j.ecolecon.2009.11.003
I've noted the so-called "luxury effect" in the distribution of biodiversity in urban areas on this blog before, as seen in the pattern of higher bird diversity in the more affluent areas of...
... Read more »
Ann P. Kinzig, Paige Warren, Chris Martin, Diane Hope, & Madhusudan Katti. (2005) The Effects of Human Socioeconomic Status and Cultural Characteristics on Urban Patterns of Biodiversity. Ecology and Society, 10(1). info:other/
I’ll be perfectly honest…I’ve been sitting on this essay from Conservation Biology for the last week or so as I mulled over my approach on breaching this topic. At one point I envisioned the title as Torn Between Ocean Science and Ocean Conservation; clearly a manifestation of the dilemma with which I was trying to [...]... Read more »
HEUPEL, M., & SIMPFENDORFER, C. (2010) Science or Slaughter: Need for Lethal Sampling of Sharks. Conservation Biology. DOI: 10.1111/j.1523-1739.2010.01491.x
'Vulture restaurants' may be excluding smaller scavengers
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Cortés-Avizanda, A., Carrete, M., & J.A. Donázar. (2010) Managing supplementary feeding for avian scavengers: Guidelines for optimal design using ecological criteria. Biological Conservation. DOI: 10.1016/j.biocon.2010.04.016
In the Fayum desert of northern Egypt, not too far from the banks of the Nile, the vestiges of ancient forests are preserved in the sand-covered strata. The fossils are ghosts of a vanished oasis in which prehistoric cousins of modern elephants wallowed in lush wetlands and a host of ancient primates scrambled through the trees, and despite being known as one of the world's best fossil sites for over a century paleontologists are continuing to discovery new species from the desert rock. The tr........ Read more »
Seiffert, E., Simons, E., Boyer, D., Perry, J., Ryan, T., & Sallam, H. (2010) A fossil primate of uncertain affinities from the earliest late Eocene of Egypt. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1001393107
How do enzymes catalyze reactions? There are countless answers of course, but one answer that has gained much attention and popularity in recent years is - through intrinsic dynamics. Is that so? PNAS recently published a paper by Arieh Warshel entitled: "Enzyme millisecond conformational dynamics do not catalyze the chemical step". Warshel, an avid assailant of the coupling between dynamics and catalysis was met by Martin Karplus, devoted advocate for catalytic dynamics, to engage in a public d........ Read more »
Pisliakov, A., Cao, J., Kamerlin, S., & Warshel, A. (2009) Enzyme millisecond conformational dynamics do not catalyze the chemical step. Proceedings of the National Academy of Sciences, 106(41), 17359-17364. DOI: 10.1073/pnas.0909150106
Kamerlin SC, & Warshel A. (2010) At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?. Proteins, 78(6), 1339-75. PMID: 20099310
Karplus, M. (2010) Role of conformation transitions in adenylate kinase. Proceedings of the National Academy of Sciences, 107(17). DOI: 10.1073/pnas.1002180107
Kamerlin, S., & Warshel, A. (2010) Reply to Karplus: Conformational dynamics have no role in the chemical step. Proceedings of the National Academy of Sciences, 107(17). DOI: 10.1073/pnas.1002658107
Henzler-Wildman KA, Lei M, Thai V, Kerns SJ, Karplus M, & Kern D. (2007) A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature, 450(7171), 913-6. PMID: 18026087
Henzler-Wildman KA, Thai V, Lei M, Ott M, Wolf-Watz M, Fenn T, Pozharski E, Wilson MA, Petsko GA, Karplus M.... (2007) Intrinsic motions along an enzymatic reaction trajectory. Nature, 450(7171), 838-44. PMID: 18026086
Wouldn't it be nice if you could improve your mental health just by eating more fish?Well, yes, it would... except for people who hate fish, who would be doomed to misery. But is it true? A new paper from Finnish researchers Suominen-Taipale et al looks at this issue: Fish Consumption and Omega-3 Polyunsaturated Fatty Acids in Relation to Depressive Episodes: A Cross-Sectional Analysis. The results are complex, but essentially, negative.The authors looked at a large sample (total n=6,500) of Fin........ Read more »
Suominen-Taipale, A., Partonen, T., Turunen, A., Männistö, S., Jula, A., & Verkasalo, P. (2010) Fish Consumption and Omega-3 Polyunsaturated Fatty Acids in Relation to Depressive Episodes: A Cross-Sectional Analysis. PLoS ONE, 5(5). DOI: 10.1371/journal.pone.0010530
Scientists have known about the feathered dinosaur Archaeopteryx for over a century and a half, but scientists are using new techniques to get a better look at this creature and its close relatives. Within the past few months alone, paleontologists have described how they have used laboratory techniques to determine what color some feathered dinosaurs [...]... Read more »
Bergmann, U., Morton, R., Manning, P., Sellers, W., Farrar, S., Huntley, K., Wogelius, R., & Larson, P. (2010) Archaeopteryx feathers and bone chemistry fully revealed via synchrotron imaging. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1001569107
This post is the first in a special series about four fundamental forces in evolution: natural selection, mutation, genetic drift, and migration.
Among non-biologists, the best-known of the Big Four forces of evolution is almost certainly natural selection. We've all heard the catchphrase "survival of the fittest," and that's a pretty good, if reductive, summing up of the principle. In more precise terms, here's how natural selection works:Natural populations of living things vary. Deer vary in........ Read more »
Grant, B., & Grant, P. (1989) Natural selection in a population of Darwin's finches. The American Naturalist, 133(3), 377-93. DOI: 10.1086/284924
Grant, P.R., & Grant, B.R. (2002) Unpredictable evolution in a 30-Year study of Darwin's finches. Science, 296(5568), 707-11. DOI: 10.1126/science.1070315
Kingsolver, J., Hoekstra, H., Hoekstra, J., Berrigan, D., Vignieri, S., Hill, C., Hoang, A., Gibert, P., & Beerli, P. (2001) The Strength of phenotypic selection in natural populations. The American Naturalist, 157(3), 245-261. DOI: 10.1086/319193
Lande, R. (1976) Natural selection and random genetic drift in phenotypic evolution. Evolution, 30(2), 314-34. DOI: 10.2307/2407703
Johnson, T., & Barton, N. (2005) Theoretical models of selection and mutation on quantitative traits. Phil. Trans. R. Soc. B, 360(1459), 1411-25. DOI: 10.1098/rstb.2005.1667
Schluter, D., & Grant, P. (1984) Determinants of morphological patterns in communities of Darwin's finches. The American Naturalist, 123(2), 175-96. DOI: 10.1086/284196
by Mary in OpenHelix
Usually when we think about comparative genomics data, we are thinking about genomes that are pretty well sequenced, and we want to look at that data with variety of tools and algorithms. But this past week we saw a question about less-well-sequenced genomes, and we thought it was an interesting inquiry. The question was: is there a web site that displays comparative karyotype data? So we went looking. And we found Chromhome.
Chromhome has a very straightforward interface. You choose a ........ Read more »
Nagarajan, S., Rens, W., Stalker, J., Cox, T., & Ferguson-Smith, M. (2008) Chromhome: A rich internet application for accessing comparative chromosome homology maps. BMC Bioinformatics, 9(1), 168. DOI: 10.1186/1471-2105-9-168
Economists in the last few years have been shifting toward testing their theoretical models, whether through the experiments of behavioral economics, or, “natural experiments.” The reason economists have had issues with testing their models is that experimentation on humans has some natural constraints. Macroeconomists have an even greater problem, as experimentation on whole societies not [...]... Read more »
Bryc K, Velez C, Karafet T, Moreno-Estrada A, Reynolds A, Auton A, Hammer M, Bustamante CD, & Ostrer H. (2010) In the Light of Evolution IV: The Human Condition Sackler Colloquium: Genome-wide patterns of population structure and admixture among Hispanic/Latino populations. Proceedings of the National Academy of Sciences of the United States of America. PMID: 20445096
... Read more »
Duggan, I. (2010) The freshwater aquarium trade as a vector for incidental invertebrate fauna. Biological Invasions. DOI: 10.1007/s10530-010-9768-x
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