Friday, 9 October 2009

Johnald's Fantastical Daily Link Splurge

Johnald's Fantastical Daily Link Splurge

Crash Into the Moon With LCROSS Friday Morning

Posted: 08 Oct 2009 04:36 PM PDT


Tomorrow morning you'll have a rare opportunity to experience a live moon crash. At 7:31 a.m. EDT, NASA's LCROSS satellite will send a rocket hurtling toward the moon at a whopping 1.55 miles per second, and a camera mounted on the spacecraft will send live footage back to Earth. Four minutes later, the entire satellite will smack into the moon, generating a giant plume of debris that should be visible from our planet with an amateur telescope.

To find out how and where to watch the carnage, check out the posts by our friends at GeekDad:

  • Ways to See LCROSS Crash on Friday Morning
  • Moon Shot Part Deux: Even More Ways of Observing the LCROSS Impact …
  • Image: Northrup Grumman

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    Your Bug-Coated Windshield Is Lousy With Genomes

    Posted: 08 Oct 2009 02:53 PM PDT


    That disgusting layer of bug guts plastered across your bumper after a road trip could also be a great way to analyze the biodiversity of where you've been.

    After a long-distance drive to a conference yielded a tremendous number of squashed bugs on his bumper, genomics researcher Anton Nekrutenko of Pennsylvania State University decided to try an experiment: Why not apply the tools of metagenomics, which is the study of DNA taken directly from an environmental sample, to the collection of insects decorating his car?

    "How many species inhabit our immediate surroundings?" wrote Nekrutenko and colleagues in a paper published Thursday in Genome Research. "A straightforward collection technique suitable for answering this question is known to anyone who has ever driven a car at highway speeds."

    By sequencing DNA taken from the bug splatter generated by two different car trips, one from Pennsylvania to Connecticut and the other from Maine to New Brunswick, Canada, the researchers discovered significant differences in insect diversity between the two regions.

    bumper_car1In addition to proving that bug carnage can provide valuable information about biodiversity, the experiment served as proof-of-principle for a new kind of metagenomic analsyis. Until now, metagenomics had been used primarily to study mixed samples of bacteria, such as the microbes that inhabit the human gut or live on the surface of our skin. But scientists are increasingly interested in applying the same shotgun analysis of genetic material to answer questions about higher organisms.

    For instance, researchers have debated for decades just how many different kinds of insects are out there, with estimates ranging from 10 million to 30 million. Of those, only a few hundred thousand have been cataloged by biologists. But analysis of insect diversity from environmental DNA samples is incredibly complex, and the researchers say our current computational tools aren't quite up to the task.

    "It's somewhat easier with bacteria because normally bacteria have small genomes, and their genomes are packed with genes that produce proteins," Nekrutenko said. Higher organisms are more complicated because they tend to have larger genomes and more "junk" DNA that doesn't code for proteins. To handle analysis of the massive amounts of data necessary to screen even a simple collection, like bugs scraped from a car, the group had to create new tools.

    "One of our main goals was technology development," Nekrutenko said. "In general, life sciences are becoming kind of like physics, very data-driven, but most biologists are not trained in data-driven research." Along with colleagues from the University of California, San Diego and Emory University, Nekrutenko's group developed a straightforward, web-based program called Galaxy that walks scientists through the steps of metagenomic analysis, from obtaining raw sequencing data to drawing up an evolutionary tree.

    Some biologists who have already started using Galaxy give it rave reviews. "My lab would be lost without it," said biologist Ross Hardison of Pennsylvania State University, who has collaborated with Nekrutenko but was not involved in this research. "We are dependent on Galaxy for a very large fraction of the analyses we do."

    Even more importantly, Nekrutenko said, Galaxy allows researchers to publish their entire dataset and methods so that other researchers can reproduce their results. "Metagenomics is kind of a parameter-dependent science," Nekrutenko said. "You run certain tools, and they have dials, and depending how you set these dials you can get completely different results. Through our system, you can see exactly how we set these dials."

    That means other researchers can repeat Nekrutenko's analysis and see if they get the same results. For instance, someone might want to double-check a particularly bizarre feature of the data: In addition to finding plenty of insect and bacterial DNA, the group uncovered genetic material from the genus Homo.

    Nekrutenko said the unexpected result probably represents an artifact: Because current databases of eukaryotic DNA sequences are dominated by the human genome, spurious human results are likely to pop up. "Precise species ID from mixed samples like this is very, very challenging," he said. "We have sequences that map to human DNA, even though I'm pretty sure we didn't kill anybody."

    Image 1: Flickr/John Beales. Image 2: A photograph of Nekrutenko's bumper after one of the bug collection trials/Anton Nekrutenko.

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    The Direction of NASA’s Future at an Impasse

    Posted: 08 Oct 2009 02:25 PM PDT


    The committee charged with rethinking American human spaceflight is done thinking, but it's still unclear what the future of NASA's astronaut corps might be, and some nagging issues have yet to be resolved.

    The U.S. Human Space Flight Plans Committee — known informally as the Augustine commission, after its head Norm Augustine, former CEO of Lockheed Martin — held its last teleconference today. The ball, or hot potato, will soon be in the Obama administration's court when the group formally presents its alternatives to the Office for Science and Technology Policy.

    "We did not rate the overall options because, first of all, we were not asked to do that — and doing it would have required that we apply some sort of judgment as to what the relative weighting of those factors should be," Augustine said.

    Even in its waning days, though, some controversies remain. The final meeting revealed some internal disputes within the group on how to "score" the alternative plans. A particularly sticky issue is the safety of the Ares I rocket, a key component of the current Constellation program.

    The safety risk the panel assigned to the various human spaceflight options was based largely on the destination of the missions — to low-Earth orbit, the moon, or elsewhere.

    The specific vehicles and systems involved in the missions were not a significant factor, said Ed Crawley, an MIT professor and committee member, in introducing the meeting.

    Still, some members, notably Bohdan Bejmuk, chair of the Constellation program Standing Review Board, argued that the Ares I should get a higher safety rating than its competitors.

    "I completely disagree with that assessment," shot back Jeff Greason, CEO of XCOR Aerospace and vice-chair of Personal Spaceflight Federation.

    Other committee members, notably Augustine himself, tried to find common ground between the panel members, but the dispute clearly remains.

    "Different partisans of different systems have arguments for why their systems should be exempt from the lessons of history," Greason said, before noting that probabilistic risk assessments based on the architecture of a particular space machine don't capture 90 percent of the accidents that have actually occurred.

    Still, Bejmuk stuck to his guns, arguing multiple times that the Ares I was intrinsically safer than the alternatives.

    "The program of record has a simpler rocket and we're not giving it credit," he contended.

    Disagreement among these experts won't make decision-making any easier for John Holdren, Obama's top science adviser, who created the panel. The panel's summary report, released in September, a few weeks later than scheduled, seemed to raise as many question as it answered. During Congressional hearings, Augustine faced heated questions from several House members who attacked the meaning and methodology of the committee's work.

    "Instead of focusing on how to strengthen the exploration program in which we have invested so much time and treasure," Gabrielle Giffords, Democrat chair of the space subcommittee a Democrat from Arizona, railed, "they gave only glancing attention to Constellation—even referring to it in the past tense in their summary report and instead spent the bulk of their time crafting alternative options that do little to illuminate the choices confronting Congress and the White House."

    Many questioned whether the Augustine commission had given enough attention to the safety of astronauts. Several others questioned the emphasis that the Augustine committee placed on working with commercial entities.

    Augustine got a kinder, almost bored reception in the Senate, but it seems clear that any plan the Obama administration may entertain to scrap the Bush-era Constellation program will face fierce criticism.

    Image: NASA/Ares I test firing.

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    The Human Genome in Three Dimensions

    Posted: 08 Oct 2009 12:16 PM PDT


    By breaking the human genome into millions of pieces and reverse-engineering their arrangement, researchers have produced the highest-resolution picture ever of the genome's three-dimensional structure.

    The picture is one of mind-blowing fractal glory, and the technique could help scientists investigate how the very shape of the genome, and not just its DNA content, affects human development and disease.

    "It's become clear that the spatial organization of chromosomes is critical for regulating the genome," said study co-author Job Dekker, a molecular biologist at the University of Massachusetts Medical School. "This opens up new aspects of gene regulation that weren't open to investigation before. It's going to lead to a lot of new questions."

    As depicted in basic biology textbooks and the public imagination, the human genome is packaged in bundles of DNA and protein on 23 chromosomes, arrayed in a neatly X-shaped form inside each cell nucleus. But that's only true during the fleeting few moments when cells are poised to divide. The rest of the time, those chromosomes exist in a dense and ever-shifting clump. Of course their constituent DNA strings are clumped, too: If the genome could be laid out end-to-end, it'd be six feet long.

    For decades, some cell biologists suspected that the genome's compression wasn't just an efficient storage mechanism, but linked to the very function and interaction of its genes. But this wasn't easy to study: Sequencing the genome destroys its shape, and electron microscopes can barely penetrate its active surface. Though its constituent parts are known, the genome's true shape has been a mystery.

    In April, a paper published in the Proceedings of the National Academy of Sciences linked patterns of gene activation to their physical proximity on chromosomes. It still provided the most persuasive evidence to date that genome shape matters, even though the researchers' chromosome map was relatively low-resolution. The topography described in the latest research, published Thursday in Science, is far more detailed.

    "It's going to change the way that people study chromosomes. It will open up the black box. We didn't know the internal organization. Now we can look at it in high resolution, try to link that structure to the activity of genes, and see how that structure changes in cells and over time," said Dekker.

    To determine genome structure without being able to directly see it, the researchers first soaked cell nuclei in formaldehyde, which interacts with DNA like glue. The formaldehyde stuck together genes that are distant from each other in linear genomic sequences, but adjacent to each other in actual three-dimensional genomic space.

    The researchers then added a chemical that dissolved the gene-by-gene linear sequence bonds, but left the formaldehyde links intact. The result was a pool of paired genes, something like a frozen ball of noodles that had been sliced into a million fragmentary layers and mixed.

    By studying the pairs, the researchers could tell which genes had been near each other in the original genome. With the aid of software that cross-referenced the gene pairs with their known sequences on the genome, they assembled a digital sculpture of the genome. And what a marvelous sculpture it is.

    "There's no knots. It's totally unentangled. It's like an incredibly dense noodle ball, but you can pull out some of the noodles and put them back in, without disturbing the structure at all," said Harvard University computational biologist Erez Lieberman-Aiden, also a study co-author.

    In mathematical terms, the pieces of the genome are folded into something similar to a Hilbert curve, one of a family of shapes that can fill a two-dimensional space without ever overlapping — and then do the same trick in three dimensions.

    How evolution arrived at this solution to the challenge of genome storage is unknown. It might be an intrinsic property of chromatin, the DNA-and-protein mix from which chromosomes are made. But whatever the origin, it's more than mathematically elegant. The researchers also found that chromosomes have two regions, one one for active genes and another for inactive genes, and the unentangled curvatures allow genes to be moved easily between them.

    Lieberman-Aden likened the configuration to the compressed rows of mechanized bookshelves found in large libraries. "They're like stacks, side-by-side and on top of each other, with no space between them. And when the genome wants to use a bunch of genes, it opens up the stack. But not only does it open the stack: it moves it to a new section of the library," he said.

    The segregation of active and inactive genes adds to evidence that genome structure affects gene function.

    "It's a great description of the structure of the nucleus, and if you put that on top of what we did, it forms the big picture," said Steven Kosak, a Northwestern University cell biologist and co-author of the April PNAS paper that linked rough outlines of chromosome arrangement to gene activation. Whereas that study only looked at a few chromosomes, the Science paper "looks at fine resolution over the whole genome," said Kosak.

    "Now you can produce these genome maps, and superimpose them with genome-wide analyses of gene expression. You can really start asking how changes in spatial organization relate to changes in genes turning on and off," said Tom Misteli, a National Cancer Institute cell biologist who studies how glitches in chromosome structure may turn cells cancerous. Neither Misteli nor Kosak were involved in the Science study.

    Connecting genome shape to gene function could also help explain the connection between genes and disease, which remain largely unexplained by traditional, sequence-focused genomics.

    "It's perfectly reasonable and almost inevitable that the 3-D structure of DNA is going to influence how it functions," said Teri Manolio, director of the National Human Genome Research Institute's Office of Population Genomics.

    Researchers also want to study how genome shape is altered. That appears to happen constantly during the transition from stem cell to adult cell, and then during cell function.

    "How much variation is there in structure across cell types? What controls it? Exactly how important is it? We don't know," said Dekker. "This is a new area of science."

    Image: From Science, a two-dimensional Hilbert curve, and the three-dimensional shape of a genome.

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    Citation: "Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome." Erez Lieberman-Aiden, Nynke L. van Berkum, Louise Williams, Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, Bryan R. Lajoie, Peter J. Sabo, Michael O. Dorschner, Richard Sandstrom, Bradley Bernstein, M. A. Bender, MarkGroudine, Andreas Gnirke, John Stamatoyannopoulos, Leonid A. Mirny, Eric S. Lander, Job Dekker. Science, Vol. 326 No. 5950, October 9, 2009.

    Brandon Keim's Twitter stream and reportorial outtakes; Wired Science on Twitter. Brandon is currently working on a book about ecosystem and planetary tipping points.

    Pigs Use Mirrors to Find Hidden Food

    Posted: 08 Oct 2009 09:48 AM PDT


    In just five hours, an average farm pig can learn how to interpret an image in the mirror and use it to find hidden food.

    Scientists consider the ability to use a mirror a sign of complex cognitive processing and an indication of a certain level of awareness. In addition to humans and some primates, dolphins, elephants, magpies and a famous African grey parrot named Alex have all been known to retrieve objects or remove marks on their body using a mirror. Now it looks like pigs should be added to the list of clever critters that can master a mirror: After spending five hours with a mirror in their pen, seven out of eight pigs could use the reflection to find a hidden bowl of grub.

    "This is the first demonstration of the ability of pigs to use mirrors," animal behavior expert Donald Broom of the University of Cambridge wrote in an email. "Finding sophisticated learning and awareness in animals can alter the way that people think about the species and may result in better welfare in the long run." Broom co-authored the paper published this month in Animal Behaviour.

    Like most animals, pigs were immediately curious when researchers placed the shiny, reflective object in their pen. They approached the mirror until they bumped into it with their snout, and then checked to see what was behind the mirror. The pigs spent an average of 20 minutes gazing at their reflection, often turning in different directions to inspect themselves from several angles.

    "These kind of movements suggest that the pigs were correlating the movements of their body with the visual stimulus they were receiving from the mirror, and so learning the contingency between the two," biologist Louise Barrett of the University of Liverpool wrote in a commentary about the paper, also published this month in Animal Behaviour.

    After five hours with a mirror, the pigs were placed into a new test area that contained a food bowl hidden behind a barrier. Although the pigs could see the reflection of the bowl in the mirror, they couldn't see the food directly. A fan above the bowl circulated the scent of food around the room, prohibiting the pigs from smelling their way to the treat.

    Seven out of eight of the pigs with previous mirror experience spotted the reflection of the food bowl and correctly interpreted its location: Instead of searching for the food in its apparent position behind the mirror, the pigs headed around the barrier and straight for the true location of the bowl. When the researchers tested pigs with no prior mirror exposure, however, nine out of 11 of them became confused, searching behind the mirror for the food.

    "These results suggest not only that pigs learn the contingency between their own movements and their image in the mirror," Barrett wrote, "but that their knowledge incorporates the layout of the environment as well, so that they can locate objects in space."

    The researchers say their experiment is more than a nifty trick: The fact that pigs can learn to use a mirror means they are capable of a type of awareness called assessment awareness, which means they can understand the significance of a situation in relation to themselves, over a short period of time. In this case, the pigs remembered how their own movements appeared in the mirror, and were able to apply that knowledge to a separate situation involving a hidden food bowl.

    "Having a sense of self and using it is a form of assessment awareness," Broom wrote. Although the mirror experiment doesn't directly prove that pigs have a sense of self, the researchers suggest that given how quickly the pigs learn to recognize their own movements in a mirror, they may have some degree of self-awareness. "We have no conclusive evidence of a sense of self," Broom wrote, "but you might well conclude that it is likely from our results."

    Other mirror tests have been used to more directly examine an animal's sense of self — if researchers apply a yellow mark to the black feathers of a magpie, for instance, the bird will use a mirror to clean itself off. Unfortunately, Broom says the mark experiments just don't work on pigs: Pigs are so accustomed to being streaked with mud, they don't much care if researchers apply extra marks on their bodies. "We have put marks on pigs," Broom wrote. "They take little notice of them."

    Combined with a host of other research studies demonstrating the keen intelligence of pigs, the researchers hope their study will lead to better treatment of the farm animals. "If an animal is clever," Broom wrote, "it is less likely to be treated as if it is an object or a machine to produce food, and more likely to be considered as an individual of value in itself."

    Image: Flickr/The Pug Father

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