Author Archives: curiouscat

New Supercomputer for Science Research

“Jaguar is one of science’s newest and most formidable tools for advancement in science and engineering,” said Dr. Raymond L. Orbach, DOE.s Under Secretary for Science. The new capability will be added to resources available to science and engineering researchers in the USA.

80 percent of the Leadership Computing Facility resources are allocated through the United States Department of Energy’s Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program, a competitively selected, peer reviewed process open to researchers from universities, industry, government and non-profit organizations. Scientists and engineers at DOE’s Oak Ridge National Laboratory are finding an increasing variety of uses for the Cray XT system. A recent report identified 10 breakthroughs in U.S. computational science during the past year. Six of the breakthroughs involved research conducted with the Jaguar supercomputer, including a first-of-its-kind simulation of combustion processes that will be used to design more efficient automobile engines. Read the computational science report. Read full press release.

ORNL’s Jaguar fastest computer for science research

Jaguar will be used for studies of global climate change, as well as development of alternative energy sources and other types of scientific problem-solving that previously could not be attempted.

Zacharia said ORNL’s Jaguar was upgraded by adding 200 Cray XT5 cabinets – loaded with AMD quadcore processors and Cray SeaStar interconnects – to the computer’s existing 84 Cray XT4 cabinets. The combined machine resulted in the new standard for computational science.

The peak operating speed is apparently just below that of Los Alamos National Laboratory’s IBM Roadrunner system, which is designed for 1.7 petaflops. But the Jaguar reportedly has triple the memory of Roadrunner and much broader research potential.
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Because the Jaguar has come online sooner than expected, Zacharia said an alert was sent to top U.S. scientists inviting them to apply for early access to the Oak Ridge computer. Their scientific proposals will be reviewed on an accelerated timetable, he said.

The peak capability of 1.64 petaflops is attributed to 1.384 petaflops from the new Cray XT5, combined with 0.266 petaflops from the existing Cray XT4 system, Zacharia said.

How fast is a quadrillion calculations per second? “One way to understand the speed is by analogy,” Zacharia said recently. “It would take the entire population of the Earth (more than 6 billion people), each of us working a handheld calculator at the rate of one second per calculation, more than 460 years to do what Jaguar at a quadrillion can do in one day.”

Genes Counter a Bacterial Attack

Gene against bacterial attack unravelled

Humans have an innate defence system against deadly bacteria. However, how the step from gene to anti-bacterial effect occurs in the body is not yet known. To date, B. Pseudomallei, a bacterium suitable for bioweapons, had managed to elude medics. It can remain hidden in the human body for many years without being detected by the immune system. The bacteria can suddenly become activated and spread throughout the body, resulting in the patient dying from blood poisoning. AMC physician Joost Wiersinga and the Laboratory for Experimental Internal Medicine discovered which gene-protein combination renders the lethal bacteria B. pseudomallei harmless.

Wiersinga focussed on the so-called Toll-like receptors. These are the proteins that initiate the fight against pathogens. There are currently ten known Toll-like receptors which are located on the outside of immune cells, our body’s defence system. The toll-like receptors jointly function as a 10-figure alarm code. Upon coming into contact with the immune cell each bacterium enters its own Toll code. For known pathogens this sets off an alarm in the immune system and the defence mechanism is activated. Yet B. pseudomallei fools the system by entering the code of a harmless bacterium. As a result the body’s defence system remains on standby.

Yet some people are resistant: they become infected but not ill. Wiersinga found a genetic cause for this resistance. He discovered which toll receptor can fend off B. pseudomallei. He did this by rearing mice DNA in which the gene for Toll2 production was switched on and off. ‘The group where the gene for Toll2 was switched off, survived the bacterial infection’, says Wiersinga. ‘The other receptor that we investigated, Toll4, had no effect – even though for the past ten years medics had regarded this as the most important receptor.’ The ultimate aim of this study is to develop a vaccine.

PLoS paper: MyD88 Dependent Signaling Contributes to Protective Host Defense against Burkholderia pseudomallei

Marine Plankton From 100 Million Years Ago Found in Amber

photo of foraminifer in amber

Marine microorganisms have been found in amber dating from the middle of the Cretaceous period. The fossils were collected in Charente, in France. This completely unexpected discovery will deepen our understanding of these lost marine species as well as providing precious data about the coastal environment of Western France during the Cretaceous. This work was carried out by researchers at the GÃ©osciences Rennes laboratory, together with researchers from the PalÃ©obiodiversitÃ© et PalÃ©oenvironnement laboratory in Paris and the Centre de GÃ©ochimie de la Surface in Strasbourg.

Amber is a fossil resin with a reputation for preserving even the most minute details of insects and other terrestrial arthropods (spiders, scorpions, mites) that lived in resiniferous trees. The forest-based provenance of amber in theory makes it impossible for marine animals to be trapped in the resin. Nonetheless, researchers from the GÃ©osciences Rennes laboratory have discovered various inclusions of marine plankton in amber from the Mid-Cretaceous (100 to 98 million years ago). These micro-organisms are found in just a few pieces of amber among the thousands that have been studied, but show a remarkable diversity: unicellular algae, mainly diatoms found in large numbers, traces of animal plankton, such as radiolaria and a foraminifer, spiny skeletons of sponges and of echinoderms.

Foraminifera (the photo shows one in Amber) are amoeboid protists with reticulating pseudopods, fine strands of cytoplasm that branch and merge to form a dynamic net.[1] They typically produce a test, or shell, which can have either one or multiple chambers, some becoming quite elaborate in structure.[2] These shells are made of calcium carbonate (CaCO3) or agglutinated sediment particles. About 275,000 species are recognized, both living and fossil.[citation needed] They are usually less than 1 mm in size.”

Carried out together with researchers at the MusÃ©um national d’histoire naturelle, the study of diatoms pushed back by 10 to 30 million years the known date for the appearance of certain marine forms of this type of algae. This new information, taken together with recent data on molecular phylogeny, marks a huge advance in our understanding of the complex evolutionary history of diatoms.

The presence of these marine organisms in the amber is an ecological paradox. How did these marine species become stuck and then trapped in the conifers’ resin? The most likely scenario is that the forest producing the amber was very close to the coast, potentially shrouded by plankton-bearing mist or flooded by sea water during storms.

The preservation of marine organisms in amber is an exceptional asset, allowing us to deepen our understanding of these lost species and to have a clear idea about the coastal environment of Western France during the Cretaceous.

press release

Friday Cat Fun #7: Curious Cat and Boxes

See more adventures of this curious cat from Japan. Or see this one of a curious kid.

Ancient Whale Uncovered in Egyptian Desert

photo of Basilosaurus fossil

The skeleton is 18 meters (50 feet) long and was found in Wadi Hitan in the Western Sahara of Egypt. The first Basilosaurus fossil was found in 1905 but no full skeleton has been discovered until now.

The new skeleton of Basilosaurus will be shipped to Michigan for preparation and preservation, University of Michigan paleontologist Philip D. Gingerich said. It then will be replicated in a casting material suitable for reconstruction and exhibition of the complete skeleton. The original fossil bones and a complete cast will be returned to Egypt for exhibition in public museums in Cairo and in the Wadi Hitan visitors center. Gingerich also hopes that a complete cast can be mounted in the University of Michigan Exhibit Museum.

The fossil whales of Wadi Hitan were first mapped in the 1980s and 1990s during expeditions led by Gingerich, a professor at the U-M Museum of Paleontology and Department of Geological Sciences. The 1989 team discovered that Basilosaurus still retained tiny, useless legs, feet, and toes representing hind legs that were lost at a later stage of whale evolution. No skeleton was collected at the time because of the remote location of Wadi Hitan and because of the large size of the whale skeletons.

Wadi Hitan is a remote valley in which hundreds of fossil whale skeletons are being exposed by the wind. They lie trapped in a sandstone formation that represents an ancient sea bed. “Here the wind sculpts the sand into spectacular shapes, which give the valley an unusual beauty in addition to its richness in fossils,” Gingerich said.

Sea-living animals found in the Wadi Hitan desert include five species of whales, including the Dorudon atrox, presently exhibited in the University of Michigan Exhibit Museum. There are also three species of sea cows (Sirenia), two crocodiles, several turtles, and a sea snake, in addition to a large number of fossilized sharks and bony fishes.

Full press release, April 2005. Photo via: Whale Found in Egypt Desert

Google Flu Leading Indicator

Google Flu Trends

During the 2007-2008 flu season, an early version of Google Flu Trends was used to share results each week with the Epidemiology and Prevention Branch of the Influenza Division at CDC. Across each of the nine surveillance regions of the United States, we were able to accurately estimate current flu levels one to two weeks faster than published CDC reports.
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So why bother with estimates from aggregated search queries? It turns out that traditional flu surveillance systems take 1-2 weeks to collect and release surveillance data, but Google search queries can be automatically counted very quickly. By making our flu estimates available each day, Google Flu Trends may provide an early-warning system for outbreaks of influenza.

For epidemiologists, this is an exciting development, because early detection of a disease outbreak can reduce the number of people affected. If a new strain of influenza virus emerges under certain conditions, a pandemic could emerge and cause millions of deaths (as happened, for example, in 1918). Our up-to-date influenza estimates may enable public health officials and health professionals to better respond to seasonal epidemics and — though we hope never to find out — pandemics.

This is an interesting example of finding new ways to quickly access what is happening in the world. Google must be doing significant amounts of similar things to see how usage patterns can server as a leading indicator.

Backyard Wildlife: Crows

bird dives at crow

Here is an action shot of a bird diving at a crow in my backyard, presumably to get the crow to leave. I noticed this for going on for several weeks (follow link for better view of the dive-bombing bird). The crow didn’t seem to mind too much most of the time.

I visited Madison this week and saw 4 wild turkeys wandering around in a residential area. I didn’t have my camera handy however, so I didn’t get a photo 🙁 It was a strange and cool site.

Crows Carry Cameras for Science:

The cameras look through the legs of the birds, transmitting what they record to a person holding a receiver several hundred meters away.
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To understand more about how and why the crows use tools, researchers need a lot of details about their lives in the wild
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Videos included footage of the crows using plant stems as tools to probe for food and even carrying a tool from one place to another. The images showed that birds on the ground pick up just 8 bits of food an hour.

Magnetic Portals Connect Sun and Earth

Magnetic Portals Connect Sun and Earth by Dr. Tony Phillips

During the time it takes you to read this article, something will happen high overhead that until recently many scientists didn’t believe in. A magnetic portal will open, linking Earth to the sun 93 million miles away. Tons of high-energy particles may flow through the opening before it closes again, around the time you reach the end of the page.

“It’s called a flux transfer event or ‘FTE,'” says space physicist David Sibeck of the Goddard Space Flight Center. “Ten years ago I was pretty sure they didn’t exist, but now the evidence is incontrovertible.”
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Researchers have long known that the Earth and sun must be connected. Earth’s magnetosphere (the magnetic bubble that surrounds our planet) is filled with particles from the sun that arrive via the solar wind and penetrate the planet’s magnetic defenses. They enter by following magnetic field lines that can be traced from terra firma all the way back to the sun’s atmosphere.

“We used to think the connection was permanent and that solar wind could trickle into the near-Earth environment anytime the wind was active,” says Sibeck. “We were wrong. The connections are not steady at all. They are often brief, bursty and very dynamic.”
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On the dayside of Earth (the side closest to the sun), Earth’s magnetic field presses against the sun’s magnetic field. Approximately every eight minutes, the two fields briefly merge or “reconnect,” forming a portal through which particles can flow. The portal takes the form of a magnetic cylinder about as wide as Earth.

See more posts on scientific inquiry and scientists advancing our understanding of how things work.

Static Stretching Decreases Muscle Strength

Stretching: The Truth

Researchers now believe that some of the more entrenched elements of many athletes’ warm-up regimens are not only a waste of time but actually bad for you. The old presumption that holding a stretch for 20 to 30 seconds – known as static stretching – primes muscles for a workout is dead wrong. It actually weakens them.
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A well-designed warm-up starts by increasing body heat and blood flow.
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To raise the body’s temperature, a warm-up must begin with aerobic activity, usually light jogging. Most coaches and athletes have known this for years.
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Athletes who need to move rapidly in different directions, like soccer, tennis or basketball players, should do dynamic stretches that involve many parts of the body. “Spider-Man” is a particularly good drill: drop onto all fours and crawl the width of the court, as if you were climbing a wall.

Federal Circuit Decides Software No Longer Patentable

The Bilski Decision Is In: Buh-Bye [Most] Business Methods Patents

This was an appeal against a rejection of a business methods patent, and the appeals court has now agreed with the rejection. At issue was whether an abstract idea could be eligible for patent protection. The court says no.

Buh-bye business methods patents!

Court Reverses Position on Biz Methods Patents

The ruling in the case, called In re Bilski, largely disavowed the controversial State Street Bank case of 1998. There, the Federal Circuit opened the door to business method patents, which had until then been excluded from patent protection, by granting protection to a system for managing mutual fund accounts. The decision, according to its detractors — which included several members of the Supreme Court — had led to the issuance of weak patents and exposed financial services companies to high-dollar litigation over business method patents.