Replies to post #129 on Extraterrestrial

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Newfound Fossil Is Transitional between Fish and Landlubbers
Scientific American, April 06, 2006

Paleontologists working in the Canadian Arctic have discovered the fossilized remains of an animal that elucidates one of evolution's most dramatic transformations: that which produced land-going vertebrates from fish. Dubbed Tiktaalik roseae, the large, predatory fish bears a number of features found in four-limbed creatures, a group known as tetrapods.



Neil Shubin of the University of Chicago and his colleagues found Tiktaalik on Ellesmere Island, some 600 miles from the North Pole, in deposits dating to 375 million years ago. Like all fish, Tiktaalik possesses fins and scales. But it also has a number of distinctly un-piscine characteristics, including a neck, a flat, crocodilelike skull, and robust ribs. As such Tiktaalik neatly fills the gap between previously known tetrapodlike fish such as Panderichthys, which lived some 385 million years ago, and the earliest tetrapods, Ichthyostega and Acanthostega, which lived about 365 million years ago. "Tiktaalik blurs the boundary between fish and land animals," Shubin observes. "This animal is both fish and tetrapod; we jokingly call it a 'fishapod.'"

Especially significant is the anatomy of Tiktaalik's pectoral fin, which contains the makings of a proper tetrapod arm. Thanks to the spectacular three-dimensional preservation of the bones--many of which were found still articulated--and the discovery of multiple specimens, the researchers were able to estimate the range of motion of the fin bones. "Most of the major joints of the fin are functional in this fish," Shubin notes. "The shoulder, elbow and even parts of the wrist are already there and working in ways similar to the earliest land-living animals." Tiktaalik, the scientists believe, used its fins to support its body on a substrate.

That doesn't mean Tiktaalik was primarily a fish out of water, however. Today Ellesmere Island is the icy dominion of the polar bear. But 375 million years ago, as part of a supercontinent that straddled the equator, it was a subtropical delta. Based on the sedimentological profile of the rock in which Tiktaalik was found, the team posits that it spent most of its time in shallow water. "This kind of shallow stream system seems to be the place where many features of land living animals first arose," comments team member Ted Daeschler of the Academy of Natural Sciences in Philadelphia. ("Tiktaalik" is the local Inuktikuk word for a large freshwater fish seen in the shallows.)

Tiktaalik is already drawing comparisons to the iconic early bird, Archaeopteryx, for its explanatory power as a transitional fossil. But it certainly leaves room for more discoveries, especially those bridging the new gap between it and the first tetrapods, along with those that contain clues to the origin of the tetrapod hindlimb. Two papers detailing the findings, as well as an accompanying commentary, appear today in Nature.

http://www.sciam.com/article.cfm?chanID=sa003&articleID=000A040D-36A2-1434-B6A283414B7F0000

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Blue ring discovered around Uranus
By Robert Sanders, Media Relations | 06 April 2006

BERKELEY – The outermost ring of Uranus, discovered just last year, is bright blue, making it only the second known blue ring in the solar system, according to a report this week in the journal Science.



A comparison of the outer rings of Saturn (at top) and Uranus, where each system has been scaled to a common planetary radius. The recently discovered outer ring of Uranus, like that of Saturn, is blue because the material in these rings is smaller than the material in the inner, red rings. Credit: Imke de Pater, Heidi Hammel, Seran Gibbard, Mark Showalter, courtesy Science

Perhaps not coincidentally, both blue rings are associated with small moons.

"The outer ring of Saturn is blue and has Enceladus right smack at its brightest spot, and Uranus is strikingly similar, with its blue ring right on top of Mab's orbit," said Imke de Pater, professor of astronomy at the University of California, Berkeley. "The blue color says that this ring is predominantly submicron-sized material, much smaller than the material in most other rings, which appear red."

The authors of the paper in the April 7 issue of Science are de Pater, Mark Showalter of the SETI Institute in Mountain View, Calif.; Heidi B. Hammel of the Space Science Institute in Boulder, Colo.; and Seran Gibbard of Lawrence Livermore National Laboratory in California.

The similarity between these outer rings implies a similar explanation for the blue color, according to the authors. Many scientists now ascribe Saturn's blue E ring to the small dust, gas and ice particles spewed into Enceladus' orbit by newly discovered plumes on that moon's surface. However, this is unlikely to be the case with Mab, a small, dead, rocky ball, about 15 miles across - one-twentieth the diameter of Enceladus.

Instead, the astronomers suspect both rings owe their blue color to subtle forces acting on dust in the rings that allow smaller particles to survive while larger ones are recaptured by the moon.

"We know now that there is at least one way to make a blue ring that doesn't involve plumes, because Mab is surely too small to be internally active," said Showalter. He and astronomer Jack Lissauer of NASA Ames Research Center in Mountain View, Calif., discovered Mab in Hubble Space Telescope images in 2003.

The likely scenario to explain Saturn's blue ring was proposed before plumes were discovered last November as the Cassini spacecraft flew by Enceladus. As modeled for the E ring, meteoroid impacts on the surface of Enceladus scatter debris into its orbit, probably in a broad range of sizes. While the larger pieces remain within the moon's orbit and eventually are swept up by the moon, smaller particles are subject to subtle forces that push them toward or away from the planet out of the moon's orbit. These forces include pressure from sunlight, magnetic torques acting on charged dust particles, and the influence of slight variations in gravity due to the equatorial bulge of Saturn.

The net result is a broad ring of smaller particles, most less than a tenth of a micron across - a thousandth the width of a human hair - that scatter and reflect predominantly blue light.

"This model can be transferred directly to what we now see in Uranus, although we still need to understand the details of the process," de Pater said.

All other rings - those around Jupiter, Saturn, Uranus and Neptune - are reddish. Though they contain particles of many sizes that reflect many wavelengths of light, red dominates not only because larger particles - many microns to meters across - are abundant, but also because the material itself may be reddish, perhaps from iron.

"Arguing by analogy, the two outermost rings, the two rings that have satellites embedded in them, are both the blue rings. That can't be coincidental, there has to be a common thread of dynamics that is causing both of these phenomena," Showalter said.

The discovery of the blue ring came after combining ground-based near-infrared observations by the Keck Telescope in Hawaii and visible-light photos taken by the Hubble Space Telescope. De Pater, Hammel and Gibbard have observed Uranus since 2000 with the second-generation NIRC2 infrared camera using the adaptive optics system on the Keck II telescope, and in August 2005 obtained 30 new images of the planet in hopes of seeing new features as the ring plane moves edge-on to Earth.

Showalter and Lissauer, on the other hand, captured numerous visible-light images of Uranus between 2003 and 2005 with Hubble's Advanced Camera for Surveys.

Neither team realized it had captured pictures of new rings until an extensive analysis, basically piling image upon image until faint features stood out from the background. In December 2005, as Showalter and Lissauer reported finding two new rings - Uranus's 12th and 13th - and two new moons, Mab and Cupid, numbers 26 and 27, de Pater, Hammel and Gibbard reported seeing the red, innermost of the two new rings but not the outermost. The blue ring peaks in brightness about 97,700 kilometers from the planet's center, exactly at Mab's orbit.

Further analysis proved to both teams that the outer ring seen in visible light was definitely not observable in the near-infrared, and so must be blue. The analysis also showed that Mab, which like its ring could not be seen in the infrared, is probably covered with water ice, like the other outer moons of Uranus, and is probably Uranus's smallest moon.

De Pater's research is supported by the National Science Foundation and the Technology Center for Adaptive Optics at UC Santa Cruz. Hammel is supported by NASA, while Gibbard is supported by the U.S. Department of Energy's National Nuclear Security Administration.

Showalter's work is supported by NASA through the Space Telescope Science Institute.

http://www.berkeley.edu/news/media/releases/2006/04/06_bluering.shtml

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Nanopore Method Could Revolutionize Genome Sequencing
By Sherry Seethaler, April 6, 2006
UCSD Press Relaease

A team led by physicists at the University of California, San Diego has shown the feasibility of a fast, inexpensive technique to sequence DNA as it passes through tiny pores. The advance brings personalized, genome-based medicine closer to reality.



The paper, published in the April issue of the journal Nano Letters, describes a method to sequence a human genome in a matter of hours at a potentially low cost, by measuring the electrical perturbations generated by a single strand of DNA as it passes through a pore more than a thousand times smaller than the diameter of a human hair. Because sequencing a person’s genome would take several months and millions of dollars with current DNA sequencing technology, the researchers say that the new method has the potential to usher in a revolution in medicine.

“Current DNA sequencing methods are too slow and expensive for it to be realistic to sequence people’s genomes to tailor medical treatments for each individual,” said Massimiliano Di Ventra, an associate professor of physics at UCSD who directed the project. “The practical implementation of our approach could make the dream of personalizing medicine according to a person’s unique genetic makeup a reality.”

The physicists used mathematical calculations and computer modeling of the motions and electrical fluctuations of DNA molecules to determine how to distinguish each of the four different bases (A, G, C, T) that constitute a strand of DNA. They based their calculations on a pore about a nanometer in diameter made from silicon nitride—a material that is easy to work with and commonly used in nanostructures—surrounded by two pairs of tiny gold electrodes. The electrodes would record the electrical current perpendicular to the DNA strand as the DNA passed through the pore. Because each DNA base is structurally and chemically different, each base creates its own distinct electronic signature.

Previous attempts to sequence DNA using nanopores were not successful because the twisting and turning of the DNA strand introduced too much noise into the signal being recorded. The new idea takes advantage of the electric field that drives the current perpendicular to the DNA strand to reduce the structural fluctuations of DNA while it moves through the pore, thus minimizing the noise.

“If nature was very unkind, then the DNA would always fluctuate so much as it passes through the nanopore that measuring the current would not give us any information about what base is present at a particular location,” explained Michael Zwolak, a graduate student in physics at the California Institute of Technology who contributed to the study. “However, we have identified a particular way to operate the nanopore/electrode system that suppresses some of the fluctuations so they aren't so great as to destroy the distinguishability of the bases.”

The researchers caution that there are still hurdles to overcome because no one has yet made a nanopore with the required configuration of electrodes, but they think it is only a matter of time before someone successfully assembles the device. The nanopore and the electrodes have been made separately, and although it is technically challenging to bring them together, the field is advancing so rapidly that they think it should be possible in the near future.

In addition to the speed and low cost of the nanopore method, the researchers calculate that it will ultimately be significantly less error-prone than current methods.

“The DNA sequencing method we propose has the potential of having fewer errors than the present method, which is based on the Sanger method,” said Johan Lagerqvist, a graduate student in physics at UCSD and the lead author on the paper. “It should be possible to sequence strands of DNA that are tens of thousands of base pairs in length, possibly as long as an entire gene, in one pass through the nanopore. With the Sanger method it is necessary to chop the DNA into smaller pieces, copy the DNA and use multiple sequencing machines, which introduces additional sources of error.”

The study was funded by the National Science Foundation and by the National Human Genome Research Institute at the National Institutes of Health. The NIH funds are from a program launched in 2004 to encourage researchers to pursue a wide range of ideas to sequence a mammal-sized genome for $1,000. The researchers say that as physicists they take a unique approach to the problem.

“We don’t think of it as DNA, we view it as a bunch of atoms and electrons that behave in ways we can predict and manipulate,” said Di Ventra.

http://ucsdnews.ucsd.edu/newsrel/science/sfastdna.asp