thoughtomics

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69 posts · 92,869 views

This is a science blog, where I will be writing about interesting papers on evolution in an understandable fashion. I like science that's on the intersection of molecular, evolutionary and computational biology.

Lucas
69 posts

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  • December 5, 2011
  • 02:36 PM
  • 624 views

Yeti Crabs grow bacteria on their hairy claws

by Lucas in thoughtomics

Deep beneath the waters of Costa Rica, dozens of crabs are waving their claws in unison, in what seems to be a rhythmic performance. It’s almost as if these crabs are locked in a ritual dance. But these charming crabs are not dancing. They are farming. The hairy claws of these crabs are covered with [...]









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  • November 23, 2011
  • 03:54 PM
  • 573 views

Frog-killing fungus is a skin-loving hybrid

by Lucas in thoughtomics

These are not the best of times for amphibians. All around the world, populations of frogs, salamanders and newts are declining. At least 489 species (7.8% of all known amphibians) are nearing extinction. More than a hundred of these endangered species have not been seen in recent years, and have likely gone extinct already. Who [...]









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Joneson S, Stajich JE, Shiu SH, & Rosenblum EB. (2011) Genomic transition to pathogenicity in chytrid fungi. PLoS pathogens, 7(11). PMID: 22072962  

Farrer RA, Weinert LA, Bielby J, Garner TW, Balloux F, Clare F, Bosch J, Cunningham AA, Weldon C, du Preez LH.... (2011) Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage. Proceedings of the National Academy of Sciences of the United States of America, 108(46), 18732-6. PMID: 22065772  

  • November 14, 2011
  • 11:45 AM
  • 675 views

Globin duplication was the key to a healthy heartbeat

by Lucas in thoughtomics

Summary: Scientists show that vertebrate-specific globins originated in two rounds of genome duplication. We vertebrates work for our O2. Whether we’re a fish or antelope, we all have gills and lungs to filter oxygen out of air or water. We also have beating hearts to transport oxygen-rich blood to the most distant corners of our [...]









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  • November 1, 2011
  • 04:52 PM
  • 867 views

Shapeless sacks and oblong paper-knives: meet your cousins

by Lucas in thoughtomics

Few people will find delight in the dredge that is hauled from the ocean floor. But for the British biologist Ray Lankester, such hauls represented an unseen world of wonder. In his Diversions of a Naturalist he describes how an encounter with a creature from the bottom of the sea that filled him with so [...]









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  • October 16, 2011
  • 07:41 AM
  • 556 views

Reports of the Black Death’s death have been greatly exaggerated

by Lucas in thoughtomics

The plague bacteria that swept through medieval Europe had been declared extinct just over a month ago. A quick google search reveals articles with headlines such as ‘Medieval plague bacteria strain probably extinct’ and ‘Black death strain extinct’. Few writers mentioned that the original research on which they reported was a technical paper first and [...]









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Schuenemann VJ, Bos K, Dewitte S, Schmedes S, Jamieson J, Mittnik A, Forrest S, Coombes BK, Wood JW, Earn DJ.... (2011) Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death. Proceedings of the National Academy of Sciences of the United States of America, 108(38). PMID: 21876176  

Bos KI, Schuenemann VJ, Golding GB, Burbano HA, Waglechner N, Coombes BK, McPhee JB, Dewitte SN, Meyer M, Schmedes S.... (2011) A draft genome of Yersinia pestis from victims of the Black Death. Nature. PMID: 21993626  

  • October 12, 2011
  • 09:06 AM
  • 676 views

Hooks can be deceiving

by Lucas in thoughtomics

Every animal has its own parasites to worry about, but canivorous reptiles and amphibians have to deal with particularly gruesome ones. They can become infected with small, worm-like creatures called pentastomes that live inside their lungs, where they suck blood from ruptured blood vessels. Reptiles pick up the parasite when they eat infected prey. Pentastomes [...]









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  • September 29, 2011
  • 01:06 PM
  • 603 views

How to tame duplicated genes

by Lucas in thoughtomics

Cell division is like an intricate dance, where chromosomes have to follow a tight choreography. The chromosomes first have to find and pair with their partners, proceed with an exchange of  DNA and then part ways again. But like the best dancers, chromosomes sometimes make mistakes. If two paired chromosomes are not lined up properly [...]









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  • September 26, 2011
  • 05:09 PM
  • 515 views

Shapeshifting protein makes sour taste sweet

by Lucas in thoughtomics

Three years ago, a friend and I were eating a slice of lime. If we had had any normal sense of taste, the sour fruit would have made us squint our eyes and twist our faces. Instead, we just sucked the juice from the fruit without twitching a muscle. To mock sourness some more, we [...]









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Ayako Koizumi, Asami Tsuchiya, Ken-ichiro Nakajima, Keisuke Ito, Tohru Terada, Akiko Shimizu-Ibuka, Loïc Briand, Tomiko Asakura, Takuma Misaka, & Keiko Abe. (2011) Human sweet taste receptor mediates acid-induced sweetness of miraculin. Proceedings of the National Academy of Sciences. info:/10.1073/pnas.1016644108

  • September 14, 2011
  • 08:43 AM
  • 445 views

Penguins colonized Africa. Thrice.

by Lucas in thoughtomics

The history of penguins in Africa is a history of false starts. The first penguin pioneers that settled Africa millions of years ago all went extinct. But the penguins didn’t give up. They came back, swept there by ocean currents, and repopulated the African coasts. That’s what the palaeontologists Daniel Ksepka and Daniel Thomas conclude [...]









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  • August 30, 2011
  • 02:30 PM
  • 396 views

Long Lost Relative of Ticks Pops Up Again

by Lucas in thoughtomics

The most precious fluid in the world isn’t black. It’s red. According to some estimates, there are over 14,000 species of insects and other crawlers that feed on blood. Every class and order seems to have its own blood loving family member. The most famous blood sucking arachnids, eight-legged animals such as mites, spiders and [...]









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  • August 8, 2011
  • 03:00 PM
  • 538 views

On the leaves of sea lettuce, the luckiest survive

by Lucas in thoughtomics

Charles Darwin described life as an eternal struggle for existence. Species compete for a limited amount of space and resources, so only those varieties that are best adapted to their niche will survive. The logic behind this reasoning is sound, yet it doesn’t apply to microbes living on sea lettuce. This humble seaweed picks bacteria on [...]









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  • August 1, 2011
  • 08:53 AM
  • 635 views

Coconuts: not indigenous, but quite at home nevertheless

by Lucas in thoughtomics

On January 9 in 1878, the Spanish brig Providencia was en route from Cuba to Spain, but would never arrive at this destination. Although the weather was clear that day, the ship wrecked off the shores of Florida. Its cargo, 20.000 coconuts harvested on the Caribbean island of Trinidad, was scattered along the coast1. The [...]









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  • July 25, 2011
  • 09:35 AM
  • 584 views

Breaking a protein in order to fix it

by Lucas in thoughtomics

Randomness often does more harm than good. Take the phrase: “nothing in biology makes sense except in the light of evolution.” I replaced a random word in this sentence with a random, different word, and got: “nothing in biology makes sense except in doctorishness light of evolution.” Not only did this random replacement turn Dobzhanksy’s [...]









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  • July 8, 2011
  • 08:17 AM
  • 1,017 views

The end of E. coli

by Lucas in thoughtomics

E. coli‘s career in science has been stellar so far. E. coli lead a simple life as an inhabitant of our guts for thousands of years, until 20th century scientists discovered that the bacterium was easy to grow and manipulate in the lab. E. coli rose to scientific fame and became a laboratory superstar. As [...]









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Leopold SR, Sawyer SA, Whittam TS, & Tarr PI. (2011) Obscured Phylogeny and Recombinational Dormancy in Escherichia coli. BMC evolutionary biology, 11(1), 183. PMID: 21708031  

Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, Bingen E, Bonacorsi S, Bouchier C, Bouvet O.... (2009) Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS genetics, 5(1). PMID: 19165319  

Retchless, A., & Lawrence, J. (2007) Temporal Fragmentation of Speciation in Bacteria. Science, 317(5841), 1093-1096. DOI: 10.1126/science.1144876  

  • June 14, 2011
  • 09:18 AM
  • 880 views

Resurrecting ancient apples and proteins

by Lucas in thoughtomics

“It is possible to travel back in time” is a bold way to begin a scientific paper by any standard. This promising first sentence appeared in a the respectable journal Nature Structural and Molecular Biology, earlier this year. The words that follow reveal why: “at the molecular level by reconstructing proteins from extinct organisms.” When [...]... Read more »

Perez-Jimenez R, Inglés-Prieto A, Zhao ZM, Sanchez-Romero I, Alegre-Cebollada J, Kosuri P, Garcia-Manyes S, Kappock TJ, Tanokura M, Holmgren A.... (2011) Single-molecule paleoenzymology probes the chemistry of resurrected enzymes. Nature structural , 18(5), 592-6. PMID: 21460845  

  • May 23, 2011
  • 11:17 AM
  • 978 views

Why Life is like Lego

by Lucas in thoughtomics

A Lego brick on its own is nothing special. But link some of them together, and you could end up with anything from a medieval castle, to a pirate hideout or a space ship. Since 1947, the Lego company has released thousands of sets under the banner of a variety of different themes. Every one [...]... Read more »

  • May 23, 2011
  • 11:17 AM
  • 971 views

Why Life is like Lego

by Lucas in thoughtomics

A Lego brick on its own is nothing special. But link some of them together, and you could end up with anything from a medieval castle, to a pirate hideout or a space ship. Since 1947, the Lego company has released thousands of sets under the banner of a variety of different themes. Every one [...]... Read more »

  • April 25, 2011
  • 11:40 AM
  • 785 views

Out of Gondwana: the early evolution of bees

by Lucas in thoughtomics

Masonry is serious business for mason bees. They build their brood cells inside cavities such as hollow reeds, rotting wood or cracks in buildings. They first fill these cells with pollen and nectar, to feed the larvae that will grow inside, before sealing them off with a mix of mud and sand. The mud partitions [...]... Read more »

Litman JR, Danforth BN, Eardley CD, & Praz CJ. (2011) Why do leafcutter bees cut leaves? New insights into the early evolution of bees. Proceedings. Biological sciences / The Royal Society. PMID: 21490010  

  • March 16, 2011
  • 05:12 PM
  • 2,195 views

How baleen whales lost a gene and their teeth

by Lucas in thoughtomics

When a blue whale opens its mouth, tonnes of water surge in. The whale then forces the water back out with its tongue, in such a way that it flows through the baleen combs in the front of its mouth. These baleen plates can filter up to half a million calories worth of plankton, krill [...]... Read more »

Meredith RW, Gatesy J, Cheng J, & Springer MS. (2011) Pseudogenization of the tooth gene enamelysin (MMP20) in the common ancestor of extant baleen whales. Proceedings. Biological sciences / The Royal Society, 278(1708), 993-1002. PMID: 20861053  

  • March 3, 2011
  • 09:10 AM
  • 1,887 views

New family tree of worms has roots in the 19th century

by Lucas in thoughtomics

Nineteenth century biologists had a point when they divided the ringed worms into free-living hunters and sessile filter feeders. Their classification was dismissed in the 1970s, but a closer look at the genes of many different worms now shows that they were closer to the truth than their later colleagues.
The classification of worms got [...]... Read more »

FAUCHALD, K., & ROUSE, G. (1997) Polychaete systematics: Past and present. Zoologica Scripta, 26(2), 71-138. DOI: 10.1111/j.1463-6409.1997.tb00411.x  

Torsten H. Struck, Christiane Paul, Natascha Hill, Stefanie Hartmann, Christoph Hösel. (2010) Phylogenomic analyses unravel annelid evolution. Nature. info:/

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