Wednesday, October 31, 2012

Triassic Flying FIsh Found

Chinese researchers have tracked the "exceptionally well-preserved fossils" to the Middle Triassic of China (235-242 million years ago).

The Triassic period saw the re-establishment of ecosystems after the Permian mass extinction.

The fossils represent new evidence that marine ecosystems re-established more quickly than previously thought.

The Permian mass extinction had a bigger impact on the earth's ecological systems than any other mass extinction, wiping out 90-95% of marine species.

Previous studies have suggested that Triassic marine life developed more quickly than was once thought and that marine ecosystems were re-established more rapidly than terrestrial ecosystems.

The new research, published in Proceedings of the Royal Society B journal, was carried out by scientists from Peking University, the Chinese Academy of Sciences and the Zhejiang Museum of Natural History.

The study shows that the new flying fish, named Potanichthys xingyiensis, was 153mm long and had the "unusual combination of morphological features" associated with gliding strategy in fishes.

The fossils show an asymmetrical, forked caudal (tail) fin and a "four-winged" body formation: a pair of enlarged pectoral fins forming "primary wings", and a smaller pair of pelvic fins acting as "auxiliary wings", according to the study.

The fossils were discovered in Guizhou Province in south-west China. They represent the first record of the extinct Thoracopteridae family of fishes to be found in Asia.
Paper link.

New Phylogenetic Tree for Avians (Birds) Shows Speciation Rates Increasing

A Yale-led scientific team has produced the most comprehensive family tree for birds to date, connecting all living bird species — nearly 10,000 in total — and revealing surprising new details about their evolutionary history and its geographic context.

Analysis of the family tree shows when and where birds diversified — and that birds' diversification rate has increased over the last 50 million years, challenging the conventional wisdom of biodiversity experts.

"It's the first time that we have — for such a large group of species and with such a high degree of confidence — the full global picture of diversification in time and space," said biologist Walter Jetz of Yale, lead author of the team's research paper, published Oct. 31 online in the journal Nature.

He continued: "The research highlights how heterogeneously fast diversifying species groups are distributed throughout the family tree and over geographic space. Many parts of the globe have seen a variety of species groups diversify rapidly and recently. All this leads to a diversification rate in birds that has been increasing over the past 50 million years."

The researchers relied heavily on fossil and DNA data, combining them with geographical information to produce the exhaustive family tree, which includes 9,993 species known to be alive now.

"The current zeitgeist in biodiversity science is that the world can fill up quickly," says biologist and co-author Arne Mooers of Simon Fraser University in Canada. "A new distinctive group, like bumblebees or tunafish, first evolves, and, if conditions are right, it quickly radiates to produce a large number of species. These species fill up all the available niches, and then there is nowhere to go. Extinction catches up, and things begin to slow down or stall. For birds the pattern is the opposite: Speciation is actually speeding up, not slowing down."

The researchers attribute the growing rate of avian diversity to an abundance of group-specific adaptations. They hypothesize that the evolution of physical or behavioral innovations in certain groups, combined with the opening of new habitats, has enabled repeated bursts of diversification. Another likely factor has been birds' exceptional mobility, researchers said, which time and again has allowed them to colonize new regions and exploit novel ecological opportunities.

In their analysis, the researchers also expose significant geographic differences in diversification rates. They are higher in the Western Hemisphere than in the Eastern, and higher on islands than mainlands. But surprisingly, they said, there is little difference in rates between the tropics and high latitudes. Regions of especially intense recent diversification include northern North American and Eurasia and southern South America.

"This was one of the big surprises," Jetz said. "For a long time biologists have thought that the vast diversity of tropical species must at least partly be due to greater rates of net species production there. For birds we find no support for this, and groups with fast and slow diversification appear to occur there as much as in the high latitudes. Instead, the answer may lie in the tropics' older age, leading to a greater accumulation of species over time. Global phylogenies like ours will allow further tests of this and other basic hypotheses about life on Earth."

China's J-31 (or J-21) Takes Flight

The smaller stealth fighter that China is developing has taken flight. 

Tuesday, October 30, 2012

World's Largest Triceratops Skull Found?

Its rumored to be 8 ft in length.  Check for fenestrae!  That sucker might be bigger than a Torosaurus skull.

Hope it was collected on the up and up.  Probably, but given the issues other fossil dealers have had recently...

Signs of the Mayan Apocalypse: DISNEY BOUGHT LUCASFILM

Continuing its strategy of delivering exceptional creative content to audiences around the world, The Walt Disney Company (DIS) has agreed to acquire Lucasfilm Ltd. in a stock and cash transaction. Lucasfilm is 100% owned by Lucasfilm Chairman and Founder, George Lucas.

Under the terms of the agreement and based on the closing price of Disney stock on October 26, 2012, the transaction value is $4.05 billion, with Disney paying approximately half of the consideration in cash and issuing approximately 40 million shares at closing. The final consideration will be subject to customary post-closing balance sheet adjustments.

“Lucasfilm reflects the extraordinary passion, vision, and storytelling of its founder, George Lucas,” said Robert A. Iger, Chairman and Chief Executive Officer of The Walt Disney Company. “This transaction combines a world-class portfolio of content including Star Wars, one of the greatest family entertainment franchises of all time, with Disney’s unique and unparalleled creativity across multiple platforms, businesses, and markets to generate sustained growth and drive significant long-term value.”

Whoa. Just. Plain. Whoa.

Jar Jar Binks direct to video musicals coming your way.

Monday, October 29, 2012

NorAm Maastrichtian Ecosystem Was Very Fragile

The Cretaceous Period of Earth history ended with a mass extinction that wiped out numerous species, most famously the dinosaurs. A new study now finds that the structure of North American ecosystems made the extinction worse than it might have been. Researchers at the University of Chicago, the California Academy of Sciences and the Field Museum of Natural History will publish their findings Oct. 29 online in the Proceedings of the National Academy of Sciences.

The mountain-sized asteroid that left the now-buried Chicxulub impact crater on the coast of Mexico's Yucatan Peninsula is almost certainly the ultimate cause of the end-Cretaceous mass extinction, which occurred 65 million years ago. Nevertheless, "Our study suggests that the severity of the mass extinction in North America was greater because of the ecological structure of communities at the time," noted lead author Jonathan Mitchell, a Ph.D. student of UChicago's Committee on Evolutionary Biology.

Mitchell and his co-authors, Peter Roopnarine of the California Academy of Sciences and Kenneth Angielczyk of the Field Museum, reconstructed terrestrial food webs for 17 Cretaceous ecological communities. Seven of these food webs existed within two million years of the Chicxulub impact and 10 came from the preceding 13 million years.

The findings are based on a computer model showing how disturbances spread through the food web. Roopnarine developed the simulation to predict how many animal species would become extinct from a plant die-off, a likely consequence of the impact.

"Our analyses show that more species became extinct for a given plant die-off in the youngest communities," Mitchell said. "We can trace this difference in response to changes in a number of key ecological groups such as plant-eating dinosaurs like Triceratops and small mammals."

The results of Mitchell and his colleagues paint a picture of late Cretaceous North America in which pre-extinction changes to food webs — likely driven by a combination of environmental and biological factors — results in communities that were more fragile when faced with large disturbances.

"Besides shedding light on this ancient extinction, our findings imply that seemingly innocuous changes to ecosystems caused by humans might reduce the ecosystems' abilities to withstand unexpected disturbances," Roopnarine said.

The team's computer model describes all plausible diets for the animals under study. In one run, Tyrannosaurus might eat only Triceratops, while in another it eats only duck-billed dinosaurs, and in a third it might eat a more varied diet. This stems from the uncertainty regarding exactly what Cretaceous animals ate, but this uncertainty actually worked to the study's benefit.

"Using modern food webs as guides, what we have discovered is that this uncertainty is far less important to understanding ecosystem functioning than is our general knowledge of the diets and the number of different species that would have had a particular diet," Angielczyk said.

Data derived from modern food webs helped the simulations account for such phenomena as how specialized animals tend to be, or how body size relates to population size and thus their probability of extinction.

The researchers also selected for their study a large number of specific food webs from all the specific webs possible in their general framework and evaluated how this sample of webs respond to a perturbation, such as the death of plants. They used the same relationships and assumptions to create food webs across all of the different sites, which means the differences between sites just stem from differences in the data rather than from the simulation itself. This makes the simulation a fundamentally comparative method, Roopnarine noted.

"We aren't trying to say that a given ecosystem was fragile, but instead that a given ecosystem was more or less fragile than another," he said.

The computer models showed that if the asteroid hit during the 13 million years preceding the latest Cretaceous communities, there almost certainly would still have been a mass extinction, but one that likely would have been less severe in North America.
This paper ought to be interesting.  Its supposed to be released tomorrow.

Paper link.  

Recovery from the PT Extinction in the Southwest United States

Post–Permo-Triassic terrestrial vertebrate recovery: southwestern United States


1. David A. Tarailo (a,*)
2. David E. Fastovsky (a,*)


a. Department of Geosciences, University of Rhode Island, Kingston, Rhode Island 02881, United States of America

*. E-mail: and


Recovery of marine biodiversity following the Permo-Triassic extinction is thought to have been delayed relative to other mass extinctions. Terrestrial vertebrate biodiversity is said to have taken as much as 15 Myr longer to recover than the marine. The present study tests, at the scale of an individual fossil community, whether a disparity in biodiversity existed in the American Southwest, between the Moenkopi Formation, containing an early Middle Triassic (Anisian) terrestrial tetrapod fauna, and the Chinle Formation, containing a successor Late Triassic (Norian) tetrapod fauna. Taking Chinle faunal biodiversity to represent full biotic recovery, comparison of taxonomic and guild diversity of faunas from similar depositional and taphonomic environments in these two formations allowed us to assess the possibility of incipient terrestrial recovery of biodiversity in the Anisian.

Comparisons were made between the Holbrook Member fauna of the Moenkopi, a unit best characterized as a low-sinuosity medium- to coarse-grained fluvial deposit, and each of four Chinle stratigraphic units, representing fluvial settings from sandy low-sinuosity to muddy high-sinuosity. Three metrics were applied: generic and familial taxonomic diversity and guild diversity; these were compared by rarefaction. Simpson and Shannon diversity metrics augmented the analysis. Units of extraordinary preservation in the Chinle—the so-called blue layers—were removed from the analysis. In all tests the biodiversity of the Holbrook Member fauna is within the variation seen in Chinle faunas.

If the results of our study represent global conditions, they suggest that by at least early Anisian time (6 Myr after the P/T extinction) biodiversity had reached levels comparable to those seen in the Late Triassic. This potentially brings the terrestrial vertebrate recovery in line with the 4–8 Myr it took for recovery in the marine realm.

XKCD: An Idealological History of the US Congress

I have to wonder if you could properly call the Republicans of the US Civil War and immediately afterwards 'right leaning.'

Sunday, October 28, 2012

Forward Unto Dawn (web series)

I'm surprised, but I am actually enjoying this.  I used to be a big gamer guy, but I am not much of one now.  This web series has surprisingly good production values, but...

Friday, October 26, 2012

Climate Change Could Devastate Tropical Frogs

Most of the more than 6,000 species of frogs in the world lay their eggs in water. But many tropical frogs lay their eggs out of water. This behavior protects the eggs from aquatic predators, such as fish and tadpoles, but also increases their risk of drying out. Justin Touchon, post-doctoral fellow at the Smithsonian Tropical Research Institute, discovered that climate change in Panama may be altering frogs' course of evolution.

By analyzing long-term rainfall data collected by the Panama Canal Authority, Touchon discovered that rainfall patterns are changing just as climate-change models predict.

"Over the past four decades, rainfall has become more sporadic during the wet season," said Touchon. "The number of rainy days decreased, and the number of gaps between storms increased."

The eggs of the pantless treefrog, Dendropsophus ebraccatus, are extremely susceptible to drying. The embryos die within a day when there is no rain. Heavy rains trigger breeding, so as storms become sporadic, the chance of rain within a day of being laid decrease and so does egg survival.

As weather patterns have changed, the advantage of laying eggs out of water has decreased, not only for pantless treefrogs but potentially for many species. "Pantless treefrogs can switch between laying eggs in water or on leaves, so they may weather the changes we are seeing in rainfall better than other species that have lost the ability to lay eggs in water," said Touchon. "Being flexible in where they put their eggs gives them more options and allows them to make decisions in a given habitat that will increase the survival of their offspring."

Looking Increasingly Like Feathers are Basal to Theropods

Because they have found orinithomimiosaurs with feathers now.  They really were ostriches with LOOOONG tails.

Thursday, October 25, 2012

Australopithecus afarensis Were Not Wholly Terrestrial

Australopithecus afarensis (the species of the well-known “Lucy” skeleton) was an upright walking species, but the question of whether it also spent much of its time in trees has been the subject of much debate, partly because a complete set of A. afarensis shoulder blades has never before been available for study. For the first time, Midwestern University Professor David Green and Curator of Anthropology at the California Academy of Sciences, Zeresenay Alemseged, have thoroughly examined the two complete shoulder blades of the fossil "Selam," an exceptionally well-preserved skeleton of an A. afarensis child from Dikika, Ethiopia, discovered in 2000 by Dr. Alemseged. Further preparation and extensive analyses of these rare bones showed them to be quite apelike, suggesting that this species was adapted to climbing trees in addition to walking bipedally when on the ground. "The question as to whether Australopithecus afarensis was strictly bipedal or if they also climbed trees has been intensely debated for more than thirty years," said Dr. Green. "These remarkable fossils provide strong evidence that these individuals were still climbing at this stage in human evolution." The new findings are published in the October 26 issue of the journal Science.

Dr. Alemseged, assisted by Kenyan lab technician Christopher Kiarie, spent 11 years carefully extracting the two shoulder blades from the rest of the skeleton, which was encased in a sandstone block. "Because shoulder blades are paper-thin, they rarely fossilize--and when they do, they are almost always fragmentary," said Dr. Alemseged. "So finding both shoulder blades completely intact and attached to a skeleton of a known and pivotal species was like hitting the jackpot. This study moves us a step closer toward answering the question 'When did our ancestors abandon climbing behavior?' It appears that this happened much later than many researchers have previously suggested."

Selam was a three-year-old A. afarensis girl who lived about 3.3 million years ago, and she represents the most complete skeleton of her kind to date. After freeing the shoulder blades from the surrounding rock, Green and Alemseged digitized them using a Microscribe, and then took detailed measurements to characterize their shape and function, comparing them to the rare shoulder fossils of other early human relatives: Homo ergaster ("Turkana Boy"), Homo floresiensis ("The Hobbit"), A. africanus, and two adult specimens of A. afarensis. They also made comparisons with an extensive modern sample of juvenile and adult chimpanzee, gorilla, orangutan, and human specimens.

The analysis of the shape and function of the bones revealed that A. afarensis shoulder blades are apelike, indicating a partially arboreal lifestyle. Drs. Green and Alemseged also found that, like living apes, the shoulder anatomy of juvenile and adult representatives of A. afarensis were quite similar. "Human scapulae change shape throughout ontogeny in a significantly different manner than closely related apes," said Dr. Green. "When we compared Selam's scapula with adult members of Australopithecus afarensis, it was clear that the pattern of growth was more consistent with that of apes than humans." At the same time, most researchers agree that many traits of the A. afarensis hip bone, lower limb, and foot are unequivocally humanlike and adapted for upright walking. "This new find confirms the pivotal place that Lucy and Selam's species occupies in human evolution," said Dr. Alemseged. "While bipedal like humans, A. afarensis was still a capable climber. Though not fully human, A. afarensis was clearly on its way."

PAK-FA(T-50) Delayed

In terms of strike aircraft, the air force is placing a big bet on the T-50 fifth generation strike fighter. Sixty of these planes are expected to be procured starting in 2016 (originally planned for 2014). While four T-50 prototypes are already being tested by the air force, by all indications new engines and advanced electronic systems (and especially its avionics) are not yet ready. This may lead to another round of delays in serial production.
 Swiped from Russian Military Reform.

As the US has found the 5th generation fighter technologies area bit tougher to develop than those that came before.  Given our experience with the F-22 and now F-35s, no one ought to be surprised that the PAK-FA/T-50 has slipped in its development & procurement schedule.  As the author notes, there is likely to be another procurement slip as well.  It may be that the entire project may slip as much as a decade: 2024 procurements rather than 2014.  That's not a dig at the Russians.  They are coming from behind (as are the Chinese) as far as experience in developing these associated $tech and its tough.  If anything the US ought to be embarrassed by its uber slippages, especially with the F-35.

Casimir Effect on a Chip!

One of the strangest effects to arise from the quantum nature of the universe is the Casimir force. This pushes two parallel conducting plates together when they are just a few dozen nanometres apart.

At these kinds of scales, the Casimir force can dominate and engineers are well aware of its unwanted effects. One reason why microelectromechanical machines have never reached their original promise is the stiction that Casimir forces can generate.

On the other hand, many engineers hope to exploit the Casimir force. Various theoretical models predict that the force should be repulsive between objects of certain shapes, a phenomenon that could prevent stiction.

But there is a problem: Casimir force experiments are extremely hard to do. One headache is that nobody has perfected the technology to position different objects accurately with a nanometre scale gap. Another is that microscopic objects tend to warp and bend; any corrugations on a flat surface can dramatically change the amount of Casimir force between them and even its direction. That makes experimental results hard to interpret.

Today, Jie Zou at the University of Florida and a few buddies take a big step towards changing this. These guys have carved a single device out of silicon that is capable of measuring the Casimir force between a pair of parallel silicon beams, the first on-chip device capable of doing this.

The device consists of one fixed beam and another moveable one attached to an electromechanical actuator. The team starts by measuring the separation between them using a scanning electron microscope. They then apply a voltage to the actuator, which pushes the movable beam towards the fixed beam.

The beams oscillate at a natural frequency, which Zou and co can easily measure. However, this frequency depends on the forces on the beams. So as the beams move closer together and the Casimir forces changes, so too does the oscillation frequency. This is how Zou and co measure the force.

Of course, there are other forces at play here too, such as residual electrostatic forces. When Zou and co take these into account, their results more or less exactly match theoretical predictions for the Casimir force that beams of this shape should generate.

German Contrarians! Hippos That Shrink in Colder Climates

Giant German hippopotamuses wallowing on the banks of the Elbe are not a common sight. Yet 1.8 million years ago hippos were a prominent part of European wildlife, when mega-fauna such as woolly mammoths and giant cave bears bestrode the continent. Now palaeontologists writing in Boreas, believe that the changing climate during the Pleistocene Era may have forced Europe's hippos to shrink to pygmy sizes before driving them to warmer climes.

"Species of hippo ranged across pre-historic Europe, including the giant Hippopotamus antiquus a huge animal which often weighed up to a tonne more than today's African hippos," said lead author Dr Paul Mazza from the University of Florence. "While these giants ranged across Spain, Italy and Germany, ancestors of the modern Hippo, Hippopotamus amphibius, reached as far north as the British Isles."

Hippos were a constant feature of European wildlife for 1.4 million years, during the climatically turbulent time of the Pleistocene era, which witnessed 17 glacial events. The experience of such environmental changes would not have been without cost, and Dr Mazza and co-author Dr Adele Bertini, also from Florence, investigated the impact this changing climate may have incurred.

The research focused on fossils from across Europe, ranging from the German town of Untermaßfeld in Thuringia, to Castel di Guido, North of Rome, and Collecurti and Colle Lepre in Italy's Central Eastern Marche province. The fossils were compared to a database of measurements taken from modern African and fossil European hippos.

"The German fossil from Untermaßfeld is the largest hippo ever found in Europe, estimated to weigh up to 3.5 tonnes," said Mazza. "The Collecurti specimen was also large, but interestingly even though it was close in both time and distance to the Colle Lepre specimen the latter specimen was 25% smaller. A final specimen, an old female from Ortona in central Italy, was smaller again. It was 17% smaller than the Collecurti fossil and approximately 50% lighter."

The authors found that a clear size threshold separated hippo specimens which heralded from different parts of the Pleistocene age. The hippos from the early Pleistocene were the largest ever known while smaller specimens emerged during the middle Pleistocene. Larger specimens briefly reappeared during the late Pleistocene.

"We believe the size difference was connected to the changing environmental conditions throughout the Pleistocene," said Mazza. "The Ortona hippo, the smallest of the specimens, lived in a climate where glacial cycles turned colder, while cold steppes replaced warm ones across the Mediterranean."

The drop in temperature and rainfall during the Pleistocene caused significant changes to plant life across Europe resulting in an expansion of grassy steppes. Being grazers hippos may have been expected to thrive in this new environment. Unexpectedly they appeared to shrink, only re-attaining their past size during the warm periods of the late Pleistocene, when forests and woodland re-colonised the steppes.

During their time in Europe hippos were forced to live in habitats influenced by a general environmental trend towards cooler and drier conditions. In response hippos achieved giant sizes during warmer and relatively more humid stages, but became smaller, and even very small, under non-ideal environmental conditions.

"While hippos are normally considered indicators of warm, temperate habitats this research shows that temperature was not only the controlling factor for their ancient ancestors," concluded Mazza. "Our research suggests other factors, such as food availability, were equally important. Appreciating the importance of factors beyond temperature is of great significance as we consider how species may adapt to future ecological and environmental changes."

Most of the papers I have seen recently have been correlating smaller size for mammals for warmer temperatures and larger sizes for colder temperatures. In a way it makes sense, you run the risk of overheating the larger you are. On the flipside, its easier to freeze if you are smaller. However, those hippos in Europe don't seem to want to play with the "rules."

Wednesday, October 24, 2012

A Hypothesis on the Aquisition of Endothermy in Therapsids

The Role of Foraging Mode in the Origin of Therapsids: Implications for the Origin of Mammalian Endothermy


1. James A. Hopson (a,*)


a. Department of Organismal Biology, University of Chicago, 1027 East 57th Street, Chicago, IL 60637, USA

*. Contact at


The question of the adaptive basis for the origin of mammalian endothermy remains unresolved despite a great deal of research effort. Controversy continues over which physiological adaptations were of greatest importance in starting ectothermic nonmammalian synapsids of the Late Paleozoic on the path that culminated in modern endothermic mammals. Models of the selective basis for the origin of endothermy fall into two main categories: “thermoregulation first” and “aerobic capacity first.” Studies of lizards show a dichotomy between a low-energy “sit-and-wait” (SW) foraging mode in Iguania and a more energy-intensive “widely foraging” (WF) mode in Autarchoglossa. It is proposed that in the transition from basal synapsids (“pelycosaurs”) to therapsids, a shift from the primitive SW mode to the WF mode put the ancestors of mammals on the path to increased aerobic capacity and the ability to sustain high levels of foraging activity. Selection for increased energy expenditure disproportionately increased the amount of food energy consumed, thus improving foraging efficiency. A shift from reliance on anaerobic muscle metabolism for short but rapid dashes to capture prey to a reliance on aerobic metabolism for active searching for prey necessitated improvements of the cardiovascular system and lungs for increased aerobic capacity and greater stamina. Over time, therapsids became locked into high food requirements, which selected for improvements in aerobic metabolism, locomotor and food-processing ability, and neurosensory/behavioral specializations. Evidence of a link between maximum activity metabolism and resting (basal) metabolism in anurans and rodents suggests that further increases in aerobic activity metabolism required an increased basal metabolic rate, which led to high body temperatures and, ultimately, homeothermy. Therapsids show adaptations for increased activity, greater food-getting and food-processing ability, and higher metabolic rates than basal synapsids (“pelycosaurs”). It is argued that the “foraging mode” model is preferable to the “parental care” model of Farmer and the “correlated progression” model of Kemp for understanding the origin of mammalian endothermy.

Already More Mobile Than a Dalek: Atlas, the Proto-terminator

Take MMI, 10 years and a willing US military, and Forever Peace, here we come.

USAF CHAMP Heralds the Era of Microwave Weapons

The missile launched from the wing pylon of a B-52 heavy bomber and streaked over the desert of western Utah. At pre-set coordinates, a microwave emitter installed in the winged, jet-propelled cruise missile blasted a target building. But there was no big bang, no billowing clouds of dust and debris. Instead, the building was struck with disruptive, high-frequency microwaves.


Engineers, researchers and test personnel from Boeing, Raytheon and the Air Force Research Laboratory observed the test flight from a conference room at nearby Hill Air Force Base. A television camera mounted in a room in the unoccupied target building showed rows of desktop computers, their screens on and programs running.

When CHAMP passed overhead and activated its Raytheon-built microwave emitter, the computers went dark -- and, a moment later, so did the camera monitoring the test. "Cheers erupted in the conference room," Boeing spokesman Randy Jackson wrote in a press release published Monday.

"This technology marks a new era in modern-day warfare," Keith Coleman, the CHAMP program manager at Boeing Phantom Works, told Jackson. "In the near future, this technology may be used to render an enemy's electronic and data systems useless even before the first troops or aircraft arrive."

Word of caution is that the US military is the most dependent on electronics on the planet.

Tuesday, October 23, 2012

Dinosaur Proteins From Fossils Confirmed

Caption: T.rex (B), B. canadensis (E) and ostrich osteocytes (H) showing positive response to propidium iodide, a DNA intercalating dye.
A team of researchers from North Carolina State University and the Palo Alto Research Center (PARC) has found more evidence for the preservation of ancient dinosaur proteins, including reactivity to antibodies that target specific proteins normally found in bone cells of vertebrates. These results further rule out sample contamination, and help solidify the case for preservation of cells – and possibly DNA – in ancient remains.

Dr. Mary Schweitzer, professor of marine, earth and atmospheric sciences with a joint appointment at the North Carolina Museum of Natural Sciences, first discovered what appeared to be preserved soft tissue in a 67-million-year-old Tyrannosaurus Rex in 2005. Subsequent research revealed similar preservation in an even older (about 80-million-year-old)Brachylophosaurus canadensis. In 2007 and again in 2009, Schweitzer and colleagues used chemical and molecular analyses to confirm that the fibrous material collected from the specimens was collagen.

Schweitzer's next step was to find out if the star-shaped cellular structures within the fibrous matrix were osteocytes, or bone cells. Using techniques including microscopy, histochemistry and mass spectrometry, Schweitzer demonstrates that these cellular structures react to specific antibodies, including one – a protein known as PHEX – that is found in the osteocytes of living birds. The findings appear online in Bone and were presented last week at the annual meeting of the Society of Vertebrate Paleontology.

"The PHEX finding is important because it helps to rule out sample contamination," Schweitzer says. "Some of the antibodies that we used will react to proteins found in other vertebrate cells, but none of the antibodies react to microbes, which supports our theory that these structures are surviving osteocytes. Additionally, the antibody to PHEX will only recognize and bind to one specific site only found in mature bone cells from birds. These antibodies don't react to other proteins or cells. Because so many other lines of evidence support the dinosaur/bird relationship, finding these proteins helps make the case that these structures are dinosaurian in origin."

Schweitzer and her team also tested for the presence of DNA within the cellular structures, using an antibody that only binds to the "backbone" of DNA. The antibody reacted to small amounts of material within the "cells" of both the T. rex and the B. canadensis. To rule out the presence of microbes, they used an antibody that binds histone proteins, which bind tightly to the DNA of everything except microbes, and got another positive result. They then ran two other histochemical stains which fluoresce when they attach to DNA molecules. Those tests were also positive. These data strongly suggest that the DNA is original, but without sequence data, it is impossible to confirm that the DNA is dinosaurian.

Was the Great Oxidation Event Very Chaotic

Most researchers imagine the initial oxygenation of the ocean and atmosphere to have been something like a staircase, but with steps only going up. The first step, so the story goes, occurred around 2.4 billion years ago, and this, the so-called Great Oxidation Event, has obvious implications for the origins and evolution of the first forms of eukaryotic life. The second big step in this assumed irreversible rise occurred almost two billion years later, coinciding with the first appearances and earliest diversification of animals.

Now a team led by geochemists at the University of California, Riverside challenges the simple notion of an up-only trend for early oxygen and provides the first compelling direct evidence for a major drop in oxygen after the first rise.

"Our group is among a subset of scientists who imagine that oxygen, once it began to accumulate in the ocean-atmosphere system, may have ultimately risen to very high levels about 2.3-2.2 billion years ago, perhaps even to concentrations close to what we see today," said Timothy Lyons, a professor of biogeochemistry and the principal investigator of the project. "But unlike the posited irreversible rise favored by many, our new data point convincingly to an equally impressive, and still not well understood, fall in oxygen about 200 million years later."

According to Lyons, this drop in oxygen may have ushered in more than a billion years that were marked by a return to low-oxygen concentrations at Earth's surface, including the likelihood of an oxygen-free deep ocean.

"It is this condition that may have set the environmental stage and ultimately the clock for the advance of eukaryotic organisms and eventually animals," he said.

Study results appear online this week in the Proceedings of the National Academy of Sciences.

"The time window between 2.3 and 2.1 billion years ago is famous for the largest and longest-lived positive carbon isotope excursion in Earth history," said Noah Planavsky, a recent Ph.D. graduate from UC Riverside, current postdoctoral fellow at Caltech, and first author of the research paper.

He explained that carbon isotopes are fractionated during photosynthesis. When organic matter is buried, oxygen is released and rises in the biosphere. The burial of organic matter is tracked by the positive or heavy isotopic composition of carbon in the ocean.

"Some workers have attributed the carbon isotope excursion to something other than organic burial and associated release of oxygen," Planavsky said. "We studied the sulfur isotope composition of the same rocks used for the carbon isotope analyses — from Canada, South Africa, the U.S., and Zimbabwe — and demonstrated convincingly that the organic burial model is the best answer."

The researchers' sulfur data point to high sulfate concentrations in the ocean, which, like today, is a classic fingerprint of high oxygen levels in the ocean and atmosphere. Sulfate, the second most abundant negatively charged ion in the ocean today, remains high when the mineral pyrite oxidizes easily on the continents and is buried in relatively small amounts in the oxygen-rich ocean.

"What is equally impressive is that the rise in oxygen was followed by a dramatic fall in sulfate and therefore oxygen," Lyons said. "Why the rise and fall occurred and how that impacted the billion years or more of ocean chemistry that followed and the life within that ocean are hot topics of research."
 Paper link.

Monday, October 22, 2012

Purgatorius Was Rather Squirrel LIke

Newly discovered fossilized bones of the world’s oldest and most primitive primate – Purgatorius – reveal a tiny and agile animal that spent much of its time eating fruit and climbing trees, researchers say.

The fossils are the first known below-the-head bones for Purgatorius and previously only teeth revealed its existence.

“The ankle bones show that it had a mobile ankle joint like primates today that live in trees,” Discovery News quoted co-author Stephen Chester, a Yale University vertebrate palaeontologist, as saying.

“This mobility would have allowed for rotating the foot in different directions as it adjusted to different angles presented by tree trunks and branches.

“It also shows that the first primates did not have elongate ankles that you see in many living primates today that are thought to be related to leaping behaviours,” Chester said.

He conducted the study with colleagues Jonathan Bloch of the Florida Museum of Natural History and William Clemens, a professor emeritus at the University of California at Berkeley and a curator for the university’s Museum of Paleontology.

After analyzing the fossils, the researchers believe that the specialized ankle bones of Purgatorius played a key role in the evolutionary success of early primates.

“These new fossils support the idea that the first 10 million years of primate evolution happened in the context of an intense period of similar diversification in flowering plants, including the ability to climb in branches and collect fruits and other products of the trees at the very beginning,” Bloch said.

Baxter got it wrong. Purga wasn't a burrower.

Are there publicly available pix of the fossil?

Navy/Virginia Tech Bot Dances Gangnam Style

This is so awful while still portending our doom at the same time (if Noel's fears are confirmed).  My fears are confirmed that the horrid viral dance moves from the internet have infected the Singularity!!!

Just imagine!  An eternity of gangnam style or the Macarena! 

A Dance of Galaxies: a NASA Simulation of Galaxies and Dark Matter

How New Genes Evolve Now Demonstrated

Like job-seekers searching for a new position, living things sometimes have to pick up a new skill if they are going to succeed. Researchers from the University of California, Davis, and Uppsala University, Sweden, have shown for the first time how living organisms do this.

The observation, published Oct. 19 in the journal Science, closes an important gap in the theory of natural selection.

Scientists have long wondered how living things evolve new functions from a limited set of genes. One popular explanation is that genes duplicate by accident; the duplicate undergoes mutations and picks up a new function; and, if that new function is useful, the gene spreads.

"It's an old idea and it's clear that this happens," said John Roth, a distinguished professor of microbiology at UC Davis and co-author of the paper.

The problem, Roth said, is that it has been hard to imagine how it occurs. Natural selection is relentlessly efficient in removing mutated genes: Genes that are not positively selected are quickly lost.

How then does a newly duplicated gene stick around long enough to pick up a useful new function that would be a target for positive selection?

Experiments in Roth's laboratory and elsewhere led to a model for the origin of a novel gene by a process of "innovation, amplification and divergence." This model has now been tested by Joakim Nasvall, Lei Sun and Dan Andersson at Uppsala.

In the new model, the original gene first gains a second, weak function alongside its main activity — just as an auto mechanic, for example, might develop a side interest in computers. If conditions change such that the side activity becomes important, then selection of this side activity favors increasing the expression of the old gene. In the case of the mechanic, a slump in the auto industry or boom in the IT sector might lead her to hone her computer skills and look for an IT position.

The most common way to increase gene expression is by duplicating the gene, perhaps multiple times. Natural selection then works on all copies of the gene. Under selection, the copies accumulate mutations and recombine. Some copies develop an enhanced side function. Other copies retain their original function.

Ultimately, the cell winds up with two distinct genes, one providing each activity — and a new genetic function is born.

Did the Russians Just Kidnap an Opposition Member From Ukraine???

Russian secret services have allegedly carried out a "rendition" by plucking a Russian opposition figure, Leonid Razvozzhayev, from a Kiev street in broad daylight last Saturday and transferring him to Lefortovo prison in Moscow.

The alleged kidnapping occurred just as Ukrainian President Viktor Yanukovych was heading to Moscow to meet with Russian President Vladimir Putin on a variety of bilateral issues, including the price Russia charges Ukraine for natural gas.


Ukrainian media reports say Mr. Razvozzhayev was applying for refugee assistance at the United Nations High Commission for Refugees in Kiev on Saturday. He left the building for lunch, and never returned, although he had left his things in the office.

"We are concerned that a person has disappeared just in the middle of the day, and nobody knows what happened and how," Oleksandra Makovska, spokeswoman of Ukraine’s UNHCR office, told journalists.

On Monday, it became clear that Razvozzhayev was in a Russian jail. The official Russian news agency RIA-Novosti reported that he had already "confessed to organizing mass disorder together with his boss and other opposition members" in a purported ten-page document that has not been made public.

Russian authorities argue that Razvozzhayev gave himself up voluntarily and penned a full confession about his part in a vast anti-Kremlin conspiracy. But footage posted by the Russian Internet journal LifeNews Monday shows Razvozzhayev being led from a Moscow police building Monday and pushed into a paddy wagon, audibly shouting to reporters that he had been kidnapped and tortured.


Razvozzhayev, an aide to opposition parliamentarian Ilya Ponomaryov, was wanted by Russia's powerful Investigative Committee for questioning in connection with a developing case against his friend, left-wing street agitator Sergei Udaltsov, who is charged with trying to overthrow Mr. Putin using funds provided by the former Soviet republic of Georgia and exiled anti-Kremlin tycoons in London.

The allegations against Mr. Udaltsov were made in a "documentary" film broadcast early this month on the state-run NTV network, which included accusations that he was plotting to seize the Russian enclave of Kaliningrad, organize terrorist actions in Moscow, and commit other revolutionary disorders.

The secretly-filmed tapes that supposedly show Udaltsov conspiring with Georgian emissary Givi Targamadze also appear to show Razvozzhayev as a participant. The Investigative Committee ordered him arrested last week, but he had already fled to Ukraine.

This all hinges on how much the Ukrainian government knew. If they knew nothing, this is...bad. Very bad. If they knew and supported the move...that's bad in a different way.  Oy.

That he volunarily turned himself in and signed a confession seems...implausible at best.

Friday, October 19, 2012

Tropics Near Unihabitable in Aftermath of Permian Extinction

Lethally Hot Temperatures During the Early Triassic Greenhouse


1. Yadong Sun (a,b,*)
2. Michael M. Joachimski (c)
3. Paul B. Wignall (b)
4. Chunbo Yan (a)
5. Yanlong Chen (d)
6. Haishui Jiang (a)
7. Lina Wang (a)
8. Xulong Lai (a)


a. State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan 430074, People’s Republic of China.

b. School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK.

c. GeoZentrum Nordbayern, Universität Erlangen-Nürnberg, Schlossgarten 5, 91054 Erlangen, Germany.

d. Institute of Earth Sciences–Geology and Paleontology, University of Graz, Heinrichstrasse 26, A-8010 Graz, Austria.

* To whom correspondence should be addressed. E-mail:


Global warming is widely regarded to have played a contributing role in numerous past biotic crises. Here, we show that the end-Permian mass extinction coincided with a rapid temperature rise to exceptionally high values in the Early Triassic that were inimical to life in equatorial latitudes and suppressed ecosystem recovery. This was manifested in the loss of calcareous algae, the near-absence of fish in equatorial Tethys, and the dominance of small taxa of invertebrates during the thermal maxima. High temperatures drove most Early Triassic plants and animals out of equatorial terrestrial ecosystems and probably were a major cause of the end-Smithian crisis.
Ocean surface temperatures passed 38, maybe 40 C and the terrestrial equatorial passed 50 to 60 C.

Pop sci write up here.

The past is an alien world.

Transbay Tower Gets Final Approval

Plans for the soaring, 1,070-foot-tall Transbay Tower received their final approvals from the Planning Commission Thursday, clearing the way for construction of what will become the city's tallest building.

The decision also may have opened the door to the desperately needed funding to build what planners say will be the crown of the downtown skyline at 101 First St.

"This is the culmination of five years of work," said Paul Paradis, senior manager for Hines, the Houston developer of the tower. "It's cause for real celebration."

It's also a welcome bit of good news for Hines, which saw its deep-pocketed investment partner in the project, insurance giant MetLife, pull out this summer. Since then, a Sept. 30 deadline for Hines to provide the public Transbay Joint Powers Authority, which owns the land, with a non-refundable $5 million line of credit has passed with no action taken.

Negotiations are continuing, said Adam Alberti, spokesman for the authority.

But while Paradis declined to discuss details of the tower's financing, he said the commission's actions could provide a real boost in attracting investors.

"An entitled piece of land in San Francisco is a valuable asset and investors realize that," he said.

The 61-story tower is the centerpiece of an effort to re-envision the city's downtown.

The new office building will be part of a 145-acre Transit Center District that will include commercial high-rises, residential towers, hotels and retail space, all wrapped around a planned Transit Center that will be the hub for local and regional bus lines, as well as the underground terminus for the proposed Caltrain extension and the statewide high-speed rail line.

The new center is part of an effort to create what the plan for the area calls a "dynamic urban center." Expanding the city's traditional downtown, with its emphasis on high-density office building, to the transit-rich SoMa neighborhood would make the Transit Center "the center of downtown, reinforcing the primacy of public transit in organizing the City's development pattern."

Thursday, October 18, 2012

Another Step to Quantum Computers: A Bus for QBits

Hybrid quantum dot-superconducting resonator device. (a) Circuit schematic and micrograph of the hybrid device design. Scanning electron micrograph (b) and cross-sectional schematic view (c) of the nanowire double quantum dot (DQD). The left and right barrier gates (BL and BR), left and right plunger gates (L and R), and middle gate (M) are biased to create a double-well potential within the nanowire. The drain contact of the nanowire, D, is grounded, and the source contact, S, is connected to an antinode of the resonator, oscillating at a voltage VCavity.

Qubit-based computing exploiting spooky quantum effects like entanglement and superposition will speed up factoring and searching calculations far above what can be done with mere zero-or-one bits. To domesticate quantum weirdness, however, to make it a fit companion for mass-market electronic technology, many tricky bi-lateral and multi-lateral arrangements---among photons, electrons, circuits, cavities, etc.---need to be negotiated.

A new milestone in this forward march: a Princeton-Joint Quantum Institute (JQI) collaboration announces the successful excitation of a spin qubit using a resonant cavity. The circuit, via the cavity, senses the presence of the qubit as if it were a bit of capacitance. This result, published this week in Nature magazine (*), points toward the eventual movement of quantum information over "bus" conduits much as digital information moves over buses in conventional computers.

Uranus' Weather Revealed

In 1986, when Voyager swept past Uranus, the probe's portraits of the planet were "notoriously bland," disappointing scientists, yielding few new details of the planet and its atmosphere, and giving it a reputation as a bore of the solar system.

Now, however, thanks to a new technique applied at the Keck Observatory, Uranus is coming into sharp focus through high-resolution infrared images, revealing in incredible detail the bizarre weather of the seventh planet from the sun.

The images were released in Reno, Nev. today (Oct. 17, 2012) at a meeting of the American Astronomical Society's Division of Planetary Sciences and provide the best look to date of Uranus's complex and enigmatic weather.

The planet's deep blue-green atmosphere is thick with hydrogen, helium and methane, Uranus's primary condensable gas. Winds blow mainly east to west at speeds up to 560 miles per hour, in spite of the small amounts of energy available to drive them. Its atmosphere is almost equal to Neptune's as the coldest in our solar system with cloud-top temperatures in the minus 360-degree Fahrenheit range, cold enough to freeze methane.

Large weather systems, which are probably much less violent than the storms we know on Earth, behave in bizarre ways on Uranus, explains Larry Sromovsky, a University of Wisconsin-Madison planetary scientist who led the new study using the Keck II telescope.

"Some of these weather systems," Sromovsky notes, "stay at fixed latitudes and undergo large variations in activity. Others are seen to drift toward the planet's equator while undergoing great changes in size and shape. Better measures of the wind fields that surround these massive weather systems are the key to unraveling their mysteries."

To get a better picture of atmospheric flow on Uranus, Sromovsky and colleagues Pat Fry, also of UW-Madison, Heidi Hammel of the Association of Universities for Research in Astronomy (AURA), and Imke de Pater of the University of California at Berkeley, used new infrared techniques to detect smaller, more widely distributed weather features whose movements can help scientists trace the planet's pattern of blustery winds.


The complexity of Uranus's weather is puzzling, Sromovsky explains. The primary driving mechanism must be solar energy because there is no detectable internal energy source. "But the sun is 900 times weaker there than on Earth because it is 30 times further from the sun, so you don't have the same intensity of solar energy driving the system," explains Sromovsky. "Thus the atmosphere of Uranus must operate as a very efficient machine with very little dissipation. Yet the weather variations we see seem to defy that requirement."

The new Keck II pictures of the planet, according to Sromovsky, are the "most richly detailed views of Uranus yet obtained by any instrument on any observatory. No other telescope could come close to producing this result.

How the NRO Saved NASA's Astrophysics Program Continued

When astronomer Alan Dressler was invited to see what might be the future of NASA’s astrophysics programme, he had to leave his mobile phone behind, lest he be tempted to grab a quick snapshot. As he and a dozen others passed through the ITT Exelis facility in Rochester, New York, a guide held up a flashing red light, to warn working Exelis engineers to seal their lips in front of people without security clearance.

Their destination was the cavernous clean area of Building 1230, where two 2.4-metre telescopes, each as big as the Hubble Space Telescope and never flown, rested on low pedestals. “It seemed almost too good be true,” says Dressler, an astronomer at the Carnegie Observatories in Pasadena, California. “Things like this just don’t drop on your doorstep.”

The unexpected gift comes from the US National Reconnaissance Office (NRO), a secretive surveillance agency that built the telescopes to peer down on Earth. In June, NASA revealed that the NRO had bequeathed the scopes to the space agency because they were no longer needed. Now NASA has to figure out what it will do with them — and whether it can afford the cost of kitting them out with instruments and sending them into orbit.

This month, NASA plans to announce a science-definition team that will embark on that assessment. The team will report by April 2013 to NASA administrator Charles Bolden on the pros, cons and costs of adapting one of the telescopes for a mission to investigate dark energy, the phenomenon thought to be accelerating the expansion of the Universe. But astronomers are already encouraged. As the veil of secrecy surrounding the telescopes lifts, astronomers are beginning to size up the devices’ capabilities. And so far, they are liking what they see — so much so that they are now talking about tacking on an instrument that would detect extrasolar planets directly. “I think the enthusiasm has only increased as time has gone on,” says Dressler.

I talked about this before here here. I am still curious which spysat model this is.  I find it amusing and interesting that part of the deal is that NASA cannot point it back at Earth.

Wednesday, October 17, 2012

First World of Alpha Centauri B

European astronomers have discovered a planet with about the mass of the Earth orbiting a star in the Alpha Centauri system — the nearest to Earth. It is also the lightest exoplanet ever discovered around a star like the Sun. The planet was detected using the HARPS instrument on the 3.6-metre telescope at ESO's La Silla Observatory in Chile. The results will appear online in the journal Nature on 17 October 2012.

Alpha Centauri is one of the brightest stars in the southern skies and is the nearest stellar system to our Solar System -- only 4.3 light-years away. It is actually a triple star -- a system consisting of two stars similar to the Sun orbiting close to each other, designated Alpha Centauri A and B, and a more distant and faint red component known as Proxima Centauri [1]. Since the nineteenth century astronomers have speculated about planets orbiting these bodies, the closest possible abodes for life beyond the Solar System, but searches of increasing precision had revealed nothing. Until now.

"Our observations extended over more than four years using the HARPS instrument and have revealed a tiny, but real, signal from a planet orbiting Alpha Centauri B every 3.2 days," says Xavier Dumusque (Geneva Observatory, Switzerland and Centro de Astrofisica da Universidade do Porto, Portugal), lead author of the paper. "It's an extraordinary discovery and it has pushed our technique to the limit!"

The European team detected the planet by picking up the tiny wobbles in the motion of the star Alpha Centauri B created by the gravitational pull of the orbiting planet [2]. The effect is minute -- it causes the star to move back and forth by no more than 51 centimetres per second (1.8 km/hour), about the speed of a baby crawling. This is the highest precision ever achieved using this method.

Alpha Centauri B is very similar to the Sun but slightly smaller and less bright. The newly discovered planet, with a mass of a little more than that of the Earth [3], is orbiting about six million kilometres away from the star, much closer than Mercury is to the Sun in the Solar System. The orbit of the other bright component of the double star, Alpha Centauri A, keeps it hundreds of times further away, but it would still be a very brilliant object in the planet's skies.

The first exoplanet around a Sun-like star was found by the same team back in 1995 and since then there have been more than 800 confirmed discoveries, but most are much bigger than the Earth, and many are as big as Jupiter [4]. The challenge astronomers now face is to detect and characterise a planet of mass comparable to the Earth that is orbiting in the habitable zone [5] around another star. The first step has now been taken [6].

This is now all over the place.

Here is the paper. Here is the SciAm version of the story. Here is the Universe Today write up. I first saw the news at A Bit More Detail.

Here is the absolutely best of the lot, of course, at systemic.

Titan's Newly Found Funky Features

Radar images from NASA's Cassini spacecraft reveal some new curiosities on the surface of Saturn's mysterious moon Titan, including a nearly circular feature that resembles a giant hot cross bun and shorelines of ancient seas. The results were presented today at the American Astronomical Society's Division of Planetary Sciences conference in Reno, Nev.

Steam from baking often causes the top of bread to lift and crack. Scientists think some similar process involving heat may be at play on Titan. The image showing the bun-like mound was obtained on May 22, 2012, by Cassini's radar instrument. Scientists have seen similar terrain on Venus, where a dome-shaped region about 20 miles (30 kilometers) across has been seen at the summit of a large volcano called Kunapipi Mons. They theorize that the Titan cross, which is about 40 miles (70 kilometers) long, is also the result of fractures caused by uplift from below, possibly the result of rising magma.

"The 'hot cross bun' is a type of feature we have not seen before on Titan, showing that Titan keeps surprising us even after eight years of observations from Cassini," said Rosaly Lopes, a Cassini radar team scientist based at NASA's Jet Propulsion Laboratory, Pasadena, Calif. "The 'bun' may be the result of what is known on Earth as a laccolith, an intrusion formed by magma pushing up from below. The Henry Mountains of Utah are well-known examples of this geologic phenomenon."

Another group of Cassini scientists, led by Ellen Stofan, who is based at Proxemy Research, Rectortown, Va., has been scrutinizing radar images of Titan's southern hemisphere. Titan is the only place other than Earth that has stable liquid on its surface, though the liquids on Titan are hydrocarbon rather than water. So far, vast seas have only been seen in Titan's northern hemisphere.

A new analysis of Cassini images collected from 2008 to 2011 suggests there were once vast, shallow seas at Titan's south pole as well. Stofan and colleagues have found two good candidates for dry or mostly dry seas. One of these dry seas appears to be about 300 by 170 miles (475 by 280 kilometers) across, and perhaps a few hundred feet (meters) deep. Ontario Lacus, the largest current lake in the south, sits inside of the dry shorelines, like a shrunken version of a once-mighty sea.

Scientists led by Oded Aharonson, another radar team member based at the California Institute of Technology in Pasadena, think that cycles analogous to Earth's Croll-Milankovich cycles, which explain climate changes in terms of the way Earth orbits around the sun, are at play on Titan, too. Such cycles on Titan would cause long-term transfer of liquid hydrocarbons from pole to pole. By this model, the south pole could have been covered with extensive seas less than 50,000 years ago.

"The seas on Titan are temporary hosts for experiments in prebiotic chemistry, and we know they are cycling from one hemisphere to the other over 100,000 years," said Stofan. "I'd love to get a closer look at the seas of the north or these dry seabeds to examine the extent to which this prebiotic chemistry has developed."

The Cassini team has confirmed some of the stability of Titan's northern seas by looking at radar images from Cassini taken about one Titan season (in this case, six Earth years) apart. The newer images, from May 22, 2012, on the same flyby as the hot cross bun images, show the shorelines stayed about the same, indicating the northern lakes are not transient weather events, in contrast to the temporary darkening of parts of the equator after a rainstorm in 2010.
 Temporary lakes and seas at the equator and permanent polar seas.  Sounds like an awesome SFnal setting waiting to be written.

Tuesday, October 16, 2012

The Intragenomic Viral Hitchhikers of Extant Theropods

The genomes of birds are riddled with DNA sequences from viruses, according to a study to be published on October 16 in mBio®, the online open-access journal of the American Society for Microbiology. Analysis of these viral sequences, known as endogenous retroviruses (ERVs), can provide insights into how both hosts and viruses have evolved over the eons.

"We examined the evolution of avian retroviruses on the basis of their fossil remnants in the three avian genomes that have been completely sequenced," write the authors from Johns Hopkins University and Uppsala University, Sweden. The authors go on to say their analyses of ERVs in chicken, turkey, and zebra finch genomes reveal that birds were a hotbed of viral evolution early in their history.

All genomes are cobbled together works-in-progress. Scientists have long known that the human genome, for example, is not all human: like most every other genome studied to date, a good chunk of the DNA we call "human" is actually made up of proviruses, sequences that retroviruses have deposited there to take advantage of the cell's ability to copy DNA and translate that DNA into working proteins. These proviruses can either be inherited in the DNA we get from our parents (endogenous retroviruses), or they can be picked up during our lifetime (exogenous retroviruses).

The study reveals that millions of years ago birds were host to many different kinds of ERVs, serving as a kind of melting pot: a meeting and mingling place where viruses recombined and shared genetic information.

Unlike early studies of ERVs in chickens, which studied selected segments of the genome and uncovered only alpha-retroviruses, this study used complete genome sequences and found a great diversity of viral sequences in bird genomes, representing the same major groups as those of mammals, but exhibiting more diversity. Most of the ERVs in birds were distinct from those found in other animals, probably indicating that the viruses did not move much between different kinds of hosts.

"We conclude that avian retroviral evolution differs from that of other vertebrates," write the researchers. "Avian retroviruses seem to have evolved rather independently from the rest of the retroviruses over the last 150 million years."

Greenland is Dumping Freshwater into the North Atlantic...and its Implications

In a new study lead by Jonathan Bamber, scientists found that, over the past few decades, the melting of Greenland glaciers has been feeding an anomalous spike in North Atlantic freshwater. If it continues as it has been, in the coming years the spike will rival the effects of the Great Salinity Anomaly—a bulge of fresh water that can affect the circulation patterns of the whole Atlantic Ocean.

Here’s the background: In the late 1960s, the first Great Salinity Anomaly (GSA) formed off the eastern shores of Greenland. Formed by a spike in Arctic ice melt, the event led to the formation of a thin sheet of fresh water that floated on the typically cold, salty waters of the north Atlantic Ocean. Over the subsequent years, the anomaly drifted about the North Atlantic, first around the southern tip of Greenland, then off to the coast of Canada, then up and around, along the Gulf Stream to northern Europe. As it traveled, the freshwater pool acted as a cap, limiting the interaction between the air and the ocean.

According to Oceanus, the magazine of the Woods Hole Oceanographic Institution, “[t]he GSA acted as a sort of moving blanket, insulating different parts of the deep ocean from contact with the atmosphere as it moved around the gyre.” Similar events have happened in the decades that followed, and scientists have found that they can cause unusual temperature patterns for the United States and northern Europe, and may even affect fish populations.

The Two of Two Bombers

The United States and Russia are both seeking to replace their strategic bombers.  The US is working with a combination of bombers that date to the 1950s, 1970s/1980s and 1990s. The USAF has 76 B-52s, 66 B-1s, and 20 B-2s.  This is also true of the Russians.  The Russians have 63 Tu-95s, 151 Tu-22s Tu-22Ms (sorta strategic) and 16 Tu-160s.

The US has embarked on the Long-Range Strike Bomber and the Russians have started on the PAK-DA.  The USAF NGB is intended to enter service in 2022.  The Russians state the same thing.  The question is whether either of them are going to be doing so. The US needs to keep costs down and survive the exceedingly serious issues it has had with project management.  The Russians need to overcome the issues with the aerospace industry's massive decline and unsubstantiated and incredible (in the negative sense) boasting claims (Hypersonic bomber by 2022?  Really, guys?  Really? (as my daughter would say))

Flight Global has articles on the status of both programs here and here.

Interestingly, the Chinese, Indians and Europeans are not developing this capability.  Or perhaps the Chinese are, but are not yet talking about it.  After all, their J-20 and J-21 programs have come to light and there was at best little said about them ahead of time. 

Permian Extinction Caused by Explosive Rather Than Flood Basalt Volcanism

In a paper published in the November 2012 issue of the journal Geology, Algeo and colleagues from the China University of Geosciences track patterns of carbon isotope ratios associated with volcanic ash layers preserved in southern China rock layers. In particular, the team looked at two rock successions preserving finely layered marine deposits that record volcanic activity from before the end of the Permian period (252 million years ago) through the early part of the next geologic period, the Triassic. These successions contain layers recording events during the crisis that resulted in the extinction of some 90 percent of marine species on Earth.

"These sections have not been studied in detail geochemically," Algeo said. "Because they are deep-marine deposits, they record a very detailed and complete sequence of events. This is something you generally don't find in terrestrial or shallow-marine rocks."

The evidence, Algeo said, demonstrates a volcanic cause of the end-Permian crisis. Volcanic activity contributed to the environmental degradation that accompanied the main extinction horizon at the end of the Permian.

Some researchers have hypothesized that the biotic crisis and mass extinction were caused by the Siberian Traps, a large flood basalt province that erupted approximately 252 million years ago, coinciding more or less with the mass extinction. "This connection has been inferred on the basis of similarities in age and, thus, is circumstantial," Algeo said.

"We demonstrate for the first time that the Permian-Triassic biotic crisis was probably triggered by enormous explosive volcanic eruptions," Algeo said. "We suspect that the ash layers in the Chinese PTB sections are linked to the Siberian Traps, although more research will be needed to verify this."

At the heart of their analysis, the co-authors identify significant changes in the ratio of carbon isotopes at each ash layer in the Chinese sections. This implies large releases of isotopically light, organically derived carbon dioxide or methane with each eruptive event. "This is consistent with large-scale injection of magma into the organic-rich sediments of the West Siberian coal province," Algeo said.

According to Algeo, the Chinese deposits have to potential to clarify the mechanisms that almost wiped out all life on Earth 252 million years ago, and to help in better constraining the timing of the Siberian Traps eruptions.

In earlier research at a variety of locations around the globe, Algeo had compiled evidence that the Permian-Triassic extinction, unlike the more famous Cretaceous-Tertiary extinction in which the large dinosaurs went extinct, was a gradual process. The final extinction event may have been preceded by hundreds of thousands of years of environmental stress. The China research supports this hypothesis of gradual steps toward a dramatic extinction event. The accumulating evidence, he said, points to a very different mechanism, and a far more devastating result, than the end-Cretaceous bolide impact.

"It's becoming clear that almost every mass extinction has a different cause," Algeo said.

Link to the paper. I'm reading. While I am THRILLED that the researcher has rejected YAGUMETs, I am cautious about declaring that this EXPLAINS EVERYTHING.  Its a data point.  A strong one.  However, its not one that necessary explains everything.  Let's see how it fits into the larger picture.  With all due respect to Dr Algeo, the PT Event explanations better than coincidence that environmental degradation was the problem.

Monday, October 15, 2012

The Laughing Bear

Bear is my nickname for my son.

New Clues to the RNA-based World That Came Before

In modern biology, all life, with the exception of some viruses, uses DNA as its genetic storage mechanism. According to the "RNA-world" hypothesis, RNA appeared on Earth first, serving as both the genetic-storage material and the functional molecules for catalyzing chemical reactions, then DNA and proteins evolved much later. Unlike DNA, RNA can adopt many different molecular conformations and so it is functionally interactive on the molecular level. In the soon-to-be-published research paper, two professors of chemistry, Christine Keating and Philip Bevilacqua, and two graduate students, Christopher Strulson and Rosalynn Molden, probe one of the nagging mysteries of the RNA-world hypothesis.

"A missing piece of the RNA-world puzzle is compartmentalization," Bevilacqua said. "It's not enough to have the necessary molecules that make up RNA floating around; they need to be compartmentalized and they need to stay together without diffusing away. This packaging needs to happen in a small-enough space -- something analogous to a modern cell -- because a simple fact of chemistry is that molecules need to find each other for a chemical reaction to occur."

To test how early cell-like structures could have formed and acted to compartmentalize RNA molecules even in the absence of lipid-like molecules that make up modern cellular membranes, Strulson and Molden generated simple, non-living model "cells" in the laboratory. "Our team prepared compartments using solutions of two polymers called polyethylene glycol (PEG) and dextran," Keating explained. "These solutions form distinct polymer-rich aqueous compartments, into which molecules like RNA can become locally concentrated."

The team members found that, once the RNA was packed into the dextran-rich compartments, the molecules were able to associate physically, resulting in chemical reactions. "Interestingly, the more densely the RNA was packed, the more quickly the reactions occurred," Bevilacqua explained. "We noted an increase in the rate of chemical reactions of up to about 70-fold. Most importantly, we showed that for RNA to 'do something' -- to react chemically -- it has to be compartmentalized tightly into something like a cell. Our experiments with aqueous two-phase systems (ATPS) have shown that some compartmentalization mechanism may have provided catalysis in an early-Earth environment."

Keating added that, although the team members do not suggest that PEG and dextran were the specific polymers present on the early Earth, they provide a clue to a plausible route to compartmentalization -- phase separation. "Phase separation occurs when different types of polymers are present in solution at relatively high concentrations. Instead of mixing, the sample separates to form two distinct liquids, similar to how oil and water separate." Keating explained. "The aqueous-phase compartments we manufactured using dextran and PEG can drive biochemical reactions by increasing local reactant concentrations. So, it's possible that some other sorts of polymers might have been the molecules that drove compartmentalization on the early Earth." Strulson added that, "In addition to the RNA-world hypothesis, these results may be relevant to RNA localization and function in non-membrane compartments in modern biology."

The team members also found that the longer the string of RNA, the more densely it would be packed into the dextran compartment of the ATPS, while the shorter strings tended to be left out. "We hypothesize that this research result might indicate some kind of primitive sorting method," Bevilacqua said. "As RNA gets shorter, it tends to have less enzyme activity. So, in an early-Earth system similar to our dextran-PEG model system, the full-length, functional RNA would have been sorted and concentrated into one phase, while the shorter RNA that is not only less functional, but also threatens to inhibit important chemical reactions, would not have been included."

A World with Four Suns

A planet has been discovered orbiting in a four-star system — and no, that doesn’t mean the accommodations and conditions are excellent. It literally means four stars, where a planet is orbiting a binary star system that in turn is orbited by a second distant pair of stars. This is the first system like this that has ever been found, and its discovery demonstrates the power of citizen scientists, as it was found by joint effort of amateurs participating on the Planet Hunters website under the guidance of professional astronomers.

This is might be an extremely rare planetary setup, astronomer Meg Schwamb from Yale says, as only six planets are currently known to orbit two stars, and none of these are orbited by other stellar companions. Astronomers are calling the newly found world a ‘circumbinary’ planet.

“Circumbinary planets are the extremes of planet formation,” said Schwamb, Planet Hunters scientist and lead author of a paper about the system presented Oct. 15 at the annual meeting of the Division for Planetary Sciences of the American Astronomical Society in Reno, Nevada. “The discovery of these systems is forcing us to go back to the drawing board to understand how such planets can assemble and evolve in these dynamically challenging environments.”

The planet is called PH1, for the first confirmed planet identified by the Planet Hunters citizen scientists, but it has the nickname of Tatooine, the planet in Star Wars that orbited two suns.

Planet Hunters uses data from the Kepler spacecraft, specially designed for looking for signs of planets.