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  • May 13, 2010
  • 11:24 PM

Mitochodrial DNA in the Nucleus and Species Life Span Differences

by Reason in Fight Aging!

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 »

Muradian, K., Lehmann, G., & Fraifeld, V. (2010) NUMT (“New Mighty”) Hypothesis of Longevity. Rejuvenation Research, 13(2-3), 152-155. DOI: 10.1089/rej.2009.0974  

  • May 13, 2010
  • 03:14 PM

Cambrian survivors - weird critters which (temporarily) cheated extinction

by Laelaps in Laelaps

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 »

Van Roy, P., Orr, P., Botting, J., Muir, L., Vinther, J., Lefebvre, B., Hariri, K., & Briggs, D. (2010) Ordovician faunas of Burgess Shale type. Nature, 465(7295), 215-218. DOI: 10.1038/nature09038  

  • May 13, 2010
  • 02:41 PM

Black ghost knifefish in a strange angle

by Lucas in thoughtomics

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  

  • May 13, 2010
  • 02:30 PM

The Future is Now?

by Journal Watch Online in Journal Watch Online

Global warming may already be driving lizard populations extinct

... Read more »

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

  • May 13, 2010
  • 01:00 PM

Acidification and Extinctions

by Uncharted Atolls in Uncharted Atolls

“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 »

  • May 13, 2010
  • 08:46 AM

Health Story on Cancer Drug Sparks Heated Debate

by aviwener in Canadian Biotechnologist 2.0

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  

  • May 13, 2010
  • 08:43 AM

The Menhaden of History

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:/

  • May 13, 2010
  • 08:30 AM

When habitat destruction is extremely subtle

by Rob Goldstein in Conservation Maven

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 »

  • May 13, 2010
  • 05:00 AM

Can direct payments avert deforestation in the Brazilian Amazon?

by Rob Goldstein in Conservation Maven

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  

  • May 13, 2010
  • 04:18 AM

Even waterfowl like the green. Of the $$ kind, that is, it seems.

by Madhu in Reconciliation Ecology

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/

  • May 12, 2010
  • 08:32 PM

Killing Sharks: Is Ocean Science Compatible with Ocean Conservation?

by Scott A. in Thriving Oceans

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 »

  • May 12, 2010
  • 03:21 PM

Picked Clean

by Journal Watch Online in Journal Watch Online

'Vulture restaurants' may be excluding smaller scavengers

... Read more »

  • May 12, 2010
  • 03:12 PM

What is it? - 37 million year old fossil primate puzzles paleontologists

by Laelaps in Laelaps

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  

  • May 12, 2010
  • 02:20 PM

Is dynamics the missing link for understanding enzyme catalysis?

by Nir London in Macromolecular Modeling Blog

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  

Karplus, M. (2010) Role of conformation transitions in adenylate kinase. Proceedings of the National Academy of Sciences, 107(17). DOI: 10.1073/pnas.1002180107  

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  

Eisenmesser EZ, Bosco DA, Akke M, & Kern D. (2002) Enzyme dynamics during catalysis. Science (New York, N.Y.), 295(5559), 1520-3. PMID: 11859194  

Daniel, R., Dunn, R., Finney, J., & Smith, J. (2003) THE ROLE OF DYNAMICS IN ENZYME ACTIVITY. Annual Review of Biophysics and Biomolecular Structure, 32(1), 69-92. DOI: 10.1146/annurev.biophys.32.110601.142445  

  • May 12, 2010
  • 11:53 AM

Happiness Is Not A Fish You Can Eat

by Neuroskeptic in Neuroskeptic

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 »

  • May 12, 2010
  • 10:52 AM

X-Rays Give a New Look at Archaeopteryx

by Brian Switek in Dinosaur Tracking

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  

  • May 12, 2010
  • 10:05 AM

The "Big Four," part I: Natural selection

by Jeremy Yoder in Denim and Tweed

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 »

Futuyma, D. (1987) On the role of species in anagenesis. The American Naturalist, 130(3), 465-73. DOI: 10.1086/284724  

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  

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  

  • May 12, 2010
  • 09:15 AM

Tip of the Week: Chromhome, for karyotype level comparative genomics

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 »

  • May 12, 2010
  • 08:28 AM

The post-Columbian panmictic “natural experiment”

by Razib Khan in Gene Expression

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 »

  • May 12, 2010
  • 08:00 AM

Fish tanks as vectors for accidental introduction of exotic species

by Rob Goldstein in Conservation Maven

... Read more »

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