Archive for June, 2008

Scientists find bugs that eat waste and excrete petrol

Tuesday, June 17th, 2008

‘Major’ Dinosaur Discovery in Utah

Tuesday, June 17th, 2008


SALT LAKE CITY (AP) — A newly discovered batch of well-preserved dinosaur bones, petrified trees and even freshwater clams in southeastern Utah could provide new clues about life in the region some 150 million years ago.

The Bureau of Land Management announced the find Monday, calling the quarry near Hanksville “a major dinosaur fossil discovery.”

An excavation revealed at least four sauropods, which are long-necked, long-tailed plant-eating dinosaurs, and two carnivorous ones, according to the bureau. It may have also uncovered an herbivorous stegosaurus.

Animal burrows and petrified tree trunks 6 feet in diameter were found nearby. The site doesn’t contain any new species but offers scientists the chance to learn more about the ecology of that time, said Scott Foss, a BLM paleontologist.

The fossilized dinosaurs are from the same late Jurassic period as those at Dinosaur National Monument, which straddles the Utah-Colorado state line, and the Cleveland-Lloyd quarry near Price.

It could be a decade or so before the full importance of the Hanksville quarry is known, Foss said. “It does have the potential to match the other major quarries in Utah,” he said.

The site, roughly 50 yards wide by 200 yards long, was excavated by a team from the Burpee Museum of Natural History in Rockford, Ill. Museum officials visited the site for about a week last summer and returned this year for a three-week excavation.

The area has long been known to locals and BLM officials as a dinosaur haven. But no one knew of the site’s magnitude until excavation began.

The bones were found in a sandstone channel of an ancient river.

“The preservation of these dinosaurs is excellent,” Foss said.

The mix of dinosaurs, trees and other species in the area may help scientists piece together what life was like 145 million years to 150 million years ago, including details about the ancient climate, Foss said.

BLM plans to close the site to conduct an environmental assessment for continued work in the area. The agency isn’t disclosing the exact location of the find because of security concerns.

Detangling DNA

Saturday, June 7th, 2008
Web edition:
Deep inside our cells, the DNA that encodes the mysteries of our individuality twines into tidy little spiral staircases neatly side by side — or so we might imagine.

Consider, though, that if you scale up the nucleus of a cell to the size of a basketball, each molecule of DNA inside it would resemble fishing line more than four miles long. And now consider what happens to your iPod headphones when you cram them into a pocket: Invariably, it seems, they tangle. And they’re only a foot long!

Now you have a picture of the gargantuan task your cells face in managing the snarls that form in DNA. Storing the DNA isn’t a problem because the cell can pack each strand systematically into a tidy, tight ball. And for some tasks, the cell can just unwind the ball a bit, keeping the unruly strands in check. But when the cell needs to snip the DNA and rearrange its genetic sequence, the strands almost unavoidably kink into a tangled mess.

Researchers have found that DNA can form incredibly complex knots, sometimes with dozens of crossings. But now a pair of mathematicians has shown that DNA can only form certain kinds of knots, not any knot at all. The discovery may help biologists understand site-specific recombination, the way that cells perform surgery on their DNA.

Although we tend to think of our genetic sequence as being fixed at conception, cells occasionally need to shuffle specific bits of their DNA around. Cells might reverse a small stretch of a sequence or move a section from one strand to another. Brewer’s yeast, for example, uses recombination just before cell division to prepare its DNA to divide rapidly. Viruses use recombination to insert their own DNA into the host cell, tricking the cell into producing thousands of copies of the virus. And recombination is our tool when we create genetically engineered cells.

But the process almost always causes some nasty knots. To alter the genetic sequence, specialized enzymes grab two pieces of DNA, snip them apart, bring the ends together, reshuffle the genetic sequence between them and rejoin the ends. Because the DNA is so tightly packed together, this process often ends with strands wound around themselves or one another, forming a knot or link. Another type of enzyme cleans up the mess afterward, snipping strands, passing them through others and reattaching them until the knot is unwound.

Biologists still don’t understand very well how recombination works. “What you really want is to see an enzyme attaching to the DNA and watch it dragging it around,” says Dorothy Buck, a mathematical biologist at Imperial College London. “You want a YouTube video of the whole process, but you can’t get it.” Current technology in microbiology only allows for still images. And even getting still images of knotted DNA is very tricky.

Biologists have managed to learn some things about how recombination works, though. Buck and her collaborator Erica Flapan of Pomona College in Claremont, Calif., found three rules governing the behavior of the enzymes that perform the recombination. The precise path the enzymes take and the way they perform their surgery determines the knot that is formed. Buck and Flapan realized that their rules meant that site-specific recombination could twist the DNA only into particular knots and links, and they applied knot theory to figure out which ones they were. Only a small proportion of the very complicated knots could occur in DNA, they found.


Narrowing down the possible knots could in turn shed light back on the activities of the enzymes. Ultimately, this could help researchers use site-specific recombination to repair the faulty DNA that causes genetic diseases.

Already feeling the heat:

Saturday, June 7th, 2008
Web edition:

The United States is already feeling the effects of climate change that’s mostly caused by humans, says a long-awaited U.S. summary of climate science released May 29.

The report is “a one-stop-shop” for what’s known about causes and effects of climate change in the United States, said Sharon Hays of the White House Office of Science and Technology Policy as she introduced the document at a press conference the morning of May 29. Issued by the National Science and Technology Council and the U.S. Climate Change Science Program, the report draws on scientific papers from researchers around the globe.

The previous science assessment, required by the Global Change Research Act, came out in 2000. The required follow-up assessment has lagged, though. Today’s assessment is two days ahead of a May 31 deadline set by a federal court after environmental groups sued to demand its release.

The new report is “a wonderful example of what happens when federal scientists are given the freedom to actually do their jobs,” says Kassie Siegel of the Center for Biological Diversity. The Center joined two other groups in the suit that prompted the deadline from the U.S. District Court of the Northern District California Oakland Division in August, 2007.

“I think it’s quite a thorough and comprehensive summary of the science that’s out there,” says Mike Brklacich of Carleton University in Canada after a quick look at the report. “I didn’t read it and say ‘Oh my God, thousands of voices have been suppressed again in the science community.”

Brklacich does say he’d like to see more consideration of the interconnected effects of climate issues, but says that report’s approach is common in the field.

The assessment starts with the question of cause: “Studies that rigorously quantify the effect of different external influences on observed changes (attribution studies) conclude that most of the recent global warming is very likely due to human-generated increases in greenhouse gas concentrations,” stated the report.

Hays jousted a bit with reporters during the press conference over whether the report signals a change of heart in the administration. “It’s simply not correct to say that this is the first time we’ve recognized the link between greenhouse gases and climate change,” she said. She cited a speech in 2002 in which President Bush referred to a National Academy of Sciences report making the link. Asked about later statements that there’s debate over the cause, she said, “There has been a debate.”

The report, after dealing with the cause, lists changes already observed within the United States. Average temperatures have risen in both this and the last century. Increasingly more of the annual precipitation fell as rain rather than snow during the past five decades. Several droughts have been severe but the last 50 years overall saw a tendency toward decreasing severity and duration of droughts. Sea level has been rising 0.08 to 0.12 inches per year along most of the U.S Atlantic and Gulf coasts.

For the future, the report notes that most of the models used in the Intergovernmental Panel on Climate Change reports predict average warming in the United States this century topping 3.6 degrees Fahrenheit. Changes in five out of the 21 models used in the IPCC report shot above 7.2 degrees Fahrenheit. The report also draws on IPCC projections of global sea level rise between 7 and 23 inches this century.

In determining what all this means to Americans, the assessment pulls work from topical reports called SAPs, some of which are still to be published. Most discussion of energy to date has focused on how to reduce emissions, the report says, but climate changes will the affect these industries. In places, hydropower or nuclear plants will have less water.

Transportation will feel the difference too. Railroad tracks may buckle and highways more easily soften into ruts with hotter, more frequent and longer lasting heat spells. Coastal flooding and landslides will slam roads and rails as well as ports.

For farmers and resource managers, the new report also draws a SAP summary about agriculture released earlier in the week by the Climate Change Science Program. “We’re seeing effects happening rapidly, more rapidly than some of us expected,” says Anthony Janetos, one of the lead authors and director of the Joint Global Change Research Institute in College Park, Md.

“ An important feature of this report is that it dispels the commonly held notion that the United States and other wealthy nations will be spared the worst impacts of climate change,” says ecosystem biologist Jay Gulledge at the Pew Center on Global Climate Change in Arlington, Va. Having the wealth doesn’t mean having the will to deal the problems, he says. “The Congress and the White House have much work to do to prepare our country to deal successfully with climate change.”

Slip, Slide, Shake: GPS, seismic data yield clues about surging Antarctic glacier

Saturday, June 7th, 2008
Web edition:


Analyses of data gathered by Global Positioning System equipment atop one of Antarctica’s largest and most dynamic glaciers and by seismometers nearby suggest that friction in just one small area beneath the broad glacier regularly halts the ice’s lurching march to the sea.


Many of Antarctica’s largest ice streams — the megaglaciers that carry most of the ice draining off the continent — move at an irregular pace, first sticking in place, then surging ahead (SN: 3/31/07, p. 202). For instance, twice each day — at times related to the cycle of tides at the Antarctic coast — a large portion of the Whillans Ice Stream surges forward about 70 centimeters over the course of 25 minutes, says Matt King, a geophysicist at Newcastle University in England.


That may not sound impressive. But the total seismic energy triggered as this 200-kilometer-long, 100-kilometer-wide section of the ice stream scrapes across the underlying material is about the same as that of a magnitude-7 earthquake. Seismometers almost 1,000 kilometers away can detect the resulting ground motions, he notes.


Previous studies have suggested but not proved that surging glaciers can produce earthquakes (SN: 1/3/04, p. 14), because GPS data to record the movements of those glaciers wasn’t available. In this case, however, an array of GPS instruments atop the Whillans Ice Stream, each collecting data about 10 times each second, complemented the information gathered by seismometers in the region, he and his colleagues report in the June 5 Nature.


Each time the ice stream surged, its seaward motion began near a broad, low hump near the middle of its channel. Flow lines frozen into the ice suggest that the hump lies over a patch on the glacier bed where friction is significantly higher than under surrounding areas of the ice stream, the researchers say. And analyses of ice-penetrating radar images hint that this patch contains little if any subglacial water, which would tend to lubricate the ice stream’s flow. Together, the data indicate that the ice stream’s stick-slip behavior is largely controlled by friction in this one spot, roughly 10 kilometers wide. Resistance there prevents the glacier from flowing downhill until tidal and gravitational forces overcome the friction, the researchers speculate.


Whillans Ice Stream “is arguably the most unusual, dynamic, large glacier on Earth,” says Ted Scambos, a glaciologist at the National Snow and Ice Data Center in Boulder, Colo. The team’s research, he adds, “is a fascinating study … that shows how complex the Antarctic Ice Sheet is, and how even now we can be amazed by the interplay of some of the Earth’s most basic systems: oceans, ice and sediments.”

Microbes Clean Up Mercury: Bacteria could detoxify Native American artifacts

Saturday, June 7th, 2008
Web edition:


BOSTON — In a sequel to the smallpox-contaminated blankets hand out, museums inadvertently began another round of toxic giving to Native Americans in the 1990s — returning headdresses and other artifacts that were laced with mercury. Now scientists are looking to a microbe that converts mercury into a form that evaporates, with hopes of cleaning up the artifacts before giving back more of them to their rightful tribes.

“Do we give them something covered in mercury just to have given them their things back? No — it is not OK,” says Munira Albuthi, a microbiologist at the University of Colorado Denver who did the research to see if such a microbial method is possible. “Mercury is a potent neurotoxin.”

The neurotoxic effects of headgear laced with mercury had been recognized anecdotally for years. At Alice’s tea party, the Mad Hatter wasn’t angry — he was crazy from wearing and working with hats, which used to be cured with mercury.

The 1990 Native American Graves Protection and Repatriation Act required federal agencies and institutions to return Native American cultural items and remains to their respective peoples. But when museums began giving back ceremonial head gear and other artifacts, many of the recipients ended up ill. The specimens were laced with mercury, a component of the pesticides that museums had used for years for preservation.

Once the problem of the poisoned artifacts was recognized, scientists had to figure out a culturally sensitive means of getting rid of the toxin.

“A lot of tribes see these artifacts as live spirits — these are relatives to a lot of people,” says Albuthi, who presented the work in Boston at the 108th meeting of the American Society for Microbiology. “So we needed to use something you would be OK with using on yourself.”

Albuthi began working with Cupriavidus metallidurans, a microbe that flourishes on metal and is not dangerous to humans. It has a set of proteins that turns mercury into a form that evaporates into the air. After contaminating paper, a watery broth and auger plates with the neurotoxin, she used a pipette to put the bacterium onto the items. Seven days later, 40 percent of the mercury had been removed from the broth, 50 percent was removed from the auger plates and 60 percent was removed from the paper. Because paper is porous and organic, it is most like the specimens that museums are dealing with, she notes.

Albuthi also investigated whether different temperatures or humidities enhanced the microbes’ mercury-morphing powers. She found that the microbes worked best at room temperature and 60 percent humidity, with about 80 percent of the mercury evaporated from the items.

The experiments used mercury concentrations of 10 parts per million, which are much higher than the quantities on most museum specimens, says Albuthi. “So maybe we’ll be able to get 100 percent, if there isn’t as much to begin with,” she says.

“This is a very interesting and particularly challenging project. They were very constrained in terms of what they could treat things with,” comments Gregory Hecht, a microbiologist at Rowan University in Glassboro, N. J. “And microbes are probably the best way to get around the issue.”

Satellite catches pyroclastic flow in motion

Saturday, June 7th, 2008
Lucky Shot
Web edition:

LUCKY SHOT A satellite image of a pyroclastic flow, an avalanche of hot ash and rocks that can travel at speeds of more than 100 kilometers per hour.


An image of a pyroclastic flow, one of the quickest and deadliest phenomena related to volcanic eruptions, has finally been caught by a satellite. These ground-hugging avalanches of hot ash and rocks can sweep down a volcano’s slopes at more than 100 kilometers per hour. They last no more than a few minutes, says Avijit Gupta, a geomorphologist at the University of Leeds in England. Luckily, he notes, the ground-gazing IKONOS satellite was passing over Indonesia’s Mount Merapi while it was erupting on June 16, 2006. Although scientists previously have tried to detect pyroclastic flows in satellite images, “normally the ash cloud over the volcano blocks the view,” he says. In this instance, strong winds blew the ash plume westward, revealing the flow, Gupta and his colleagues report in the May 27 Eos. The serendipitous image captured the pyroclastic flow when it was about 500 meters long, between 250 and 500 meters wide, and 50 meters high.