Bespoke Life | Cosmic Variance

Synthetic CellCraig Venter and colleagues have achieved a remarkable milestone: they designed a genome, and brought it to life. More specifically, they’ve synthesized a chromosome consisting of over a million DNA base pairs, and implanted it in a bacterial cell to replace the cell’s original genome. That cell then reproduced, giving birth to offspring that only had the synthetic genome. See the Venter Institute press release, discussion in Nature (pdf), more discussion at Edge, and some background from Carl Zimmer. Update: and here is the paper.

Who knows exactly what this means as yet — but it’s important! You can argue if you like about whether it’s really “artificial life” — that argument has already started, and already seems boring. There are also speculations about designing microorganisms to help us solve problems like global warming or (let’s say) massive oil spills. Not completely crazy speculations, either. But there’s a long way to go before anything like that is coming off a biological assembly line. And eventually we’ll be going much further than that, beyond designer microorganisms into much weirder terrain. This isn’t a culmination, it’s just a start.


Gulf Oil Update: Good News for Florida, Bad News for Louisiana’s Wetlands | 80beats

ControlledburnWill the Florida Keys catch a break with the loop current? Most observers are now in agreement that one of the biggest ecological worries about the BP oil spill—that it could reach the Gulf of Mexico’s loop current that flows to the Keys—has begun to occur. However, The New York Times reports today via Greenwire that eddies around the edge of the current are keeping much of the oil out of it.

Clear predictions are hard to come by because the oil continues to defy expectations about which direction it will go, and so does the loop current.

The loop moves based on shifting winds and other environmental factors, so even though oil is leaking continuously it may be in the current one day, and out the next. The slick itself has defied scientists’ efforts to track it and predict its path. Instead, it has repeatedly advanced and retreated, an ominous, shape-shifting mass in the Gulf, with vast underwater lobes extending outward [AP].

And, oceanographers like Mitch Roffer say, eddies forming near the current could disrupt it and change the oil’s course.

Satellite shots this morning showed that an eddy farther south along the Florida coast is expanding in size and strength. That cyclone appears likely to destabilize or even sever the Loop Current, greatly reducing the oil threat to the Florida Keys and beyond, he said. “If it forms, it’s going to pull a lot of the oil away from Florida,” Roffer said. There are no guarantees, he added, “but it looks very likely that this is forming” [The New York Times].

While this development—if it holds—would benefit the Keys and the areas beyond, there’s still a great mass of oil dumping into the Gulf. BP said today that the siphon it successfully installed on the leak is now carrying 5,000 barrels of oil per day up to a tanker on the shore. Since lots of oil is still leaking, that’s a de facto admission that the original estimate of the spill—5,000 barrels a day—was much too low. You can now watch the live video feed of the oil online.

Another lingering fear about the spill is coming to pass as well. Oil is beginning to show up in force on the Louisiana coastline, according to Governor Bobby Jindal.

“This is serious — this is the heavy oil that everyone has been fearing. It is here now,” Jindal said Wednesday as he toured the Mississippi Delta by boat and swept a fishnet through water, holding up dark, dripping glop. The region is home to rare birds, mammals and a wide variety of marine life. “This is one of the oldest wildlife management areas here in Louisiana, and now it is covered in oil,” Jindal said [NPR].

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Related Content:
80beats: Gulf Oil Spill: Fishing Ban Extended; Endangered Turtles Threatened
80beats: Good News: BP’s Oil Siphon Is Working. Bad News: Florida Keys Are in Danger
80beats: Scientists Say Gulf Spill Is Way Worse Than Estimated. How’d We Get It So Wrong?
80beats: Testimony Highlights 3 Major Failures That Caused Gulf Spill
80beats: 5 Offshore Oil Hotspots Beyond the Gulf That Could Boom—Or Go Boom

Image: U.S Coast Guard photo by Chief Petty Officer John Kepsimelis


NASA’s Tricky, Trippy Games With the Color Spectrum | Visual Science


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Though humans cannot see light outside the visible spectrum, satellites are able to detect wavelengths into the ultraviolet and infrared. The Landsat 7 satellite uses an instrument that collects seven images at once, with each image showing a specific section of the electromagnetic spectrum, called a band. Each image highlights a different part of the electromagnetic spectrum.

The satellites original images are all acquired in black and white, so color must be assigned via computer to the black and white images. The three primary colors of light are red, green and blue, and each color is given a different band/image. Once the three images are combined, you will have what is called a “false color image.” A common band combination shows green, healthy vegetation as bright red, which is useful in forestry and agricultural applications. Landsat images are also used to gather geological and hydrological data along with other kinds of environmental monitoring. In a helpful explanation, the folks at Landsat offer this catchy formula to aid you in remembering: “One common way that primary colors are assigned to bands can be easily remembered using the mnemonic:

“RGB = NRG (Red, Green, Blue = Near Infrared, Red, Green…)
Red = Near IR (ETM+ band 4)
Green = Red (ETM+ band 3)
Blue = Green (ETM+ band 2)”

There. That should be easy to remember. My suggestion: try singing it.

All images courtesy USGS National Center for EROS and NASA Landsat Project Science Office

Ganges River Delta. The Ganges River forms an extensive delta where it empties into the Bay of Bengal.


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Zero A Capillary With a Meriam

I am trying to figure out how to zero a capillary x-mitter with my meriam 4100. I was able to adjust the zero trim, but I know that is not what I needed to do, I did it to help that vessel limp along for now. My range is -10.46 to -3.46. My zero was +7 when the flanged sensing elements were side b

U.K. Surveillance Systems Scaled Back

From CBC | Technology & Science News:

Britain's new deputy prime minister has pledged to curb the country's extensive system of official surveillance and data collection by scrapping an unpopular national identity card program, limiting the retention of DNA samples and regulating t

Scientists create first ever synthetic bacterium that looks like Craig Venter | Not Exactly Rocket Science

Venter_mycoplasma

In a move that’s been hailed as one of the greatest scientific breakthroughs of the century, a group of scientists have created a synthetic bacterium that looks like Craig Venter.

The team artificially synthesised a genome in the lab and inserted it into an empty bacterial cell, which promptly remodelled its outer wall into a picture of Venter’s face.

“Before today, there had only been one genome in the world with the right sequence of nucleotides to encode my face,” said Venter, speaking from his secret volcano lair. “Now there are two, and I can’t help but think that things have greatly improved.

“Of course, the ultimate goal is to build a creature with 100 heads, not unlike the mythical hydra, but where every head is my head.

“Or, er, something about biofuels,” he added.

Other scientists warned that the ethical debates sparked by the discovery had only begun. Andrew McQueen from New York University said, “Imagine going for a walk in the park only to find that every bird in the trees has Craig’s face on it and they’re all looking at you.”

“They’re not smiling either,” he added before curling up on the floor and crying quietly.

Meanwhile, it transpired that Venter has coded a line from a James Joyce novel into his synthetic genome, a move that drew condemnation from America’s creationist groups, who didn’t understand what a novel was.

(For actual takes on this story, see a straight take in the Times, eight glowing reactions in Nature, a more reserved take in the New York Times that more closely mirrors my own feelings, and an excellent explanation of the new paper’s technical achievements, which are indeed substantial.)

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Walgreens’ Genetic Tests on Hold, Under Congressional Investigation | 80beats

PathwayWhen Walgreens, the nation’s biggest drugstore chain, announced last week that personal genomics tests would join diet soda and pregnancy tests in its aisles, we gave some reasons that might not be such a great thing. We weren’t the only ones concerned: The Food and Drug Administration said it would investigate the tests, and now Congress is involved. It opened an investigation into personal genomics tests yesterday.

House Committee on Energy and Commerce, chaired by Rep. Henry A. Waxman, just sent out official requests for information to the big three personal genomics companies—23andMe, Navigenics, and Pathway Genomics.

Waxman’s interest was piqued by the move—quickly rescinded last week after the FDA objected—by Pathway to sell its DNA-collection kits in Walgreen’s drugstores. The letters ask the companies for information on, among other things, how they analyze test results to determine someone’s risk for any disease or drug response, and how accurately the DNA tests identify genetic risks [Newsweek].

That’s important because while sequencing someone’s genome is a rather objective task, interpreting it is not. The companies have been loath to divulge how they do the latter part, which is what Waxman’s committee wants to know. (Check out the DISCOVER Magazine feature in which our reporter has her DNA analyzed by three different companies.)

Walgreens has now delayed the introduction the Pathway tests onto its shelves. So has CVS, which planned to offer the same product beginning in August.

The kits would allow buyers to send a saliva sample to Pathway, based in San Diego, for analysis. The company’s testing fee would be based on the information the consumer wants. Pathway says its testing allows buyers to learn whether they are at risk for a range of diseases, including breast cancer and Alzheimer’s. But questions have been raised about whether most consumers would be able to interpret the results [UPI].

Meanwhile, across the country from Washington D.C., another personal DNA testing argument is in full force. On Tuesday we brought you the story that UC Berkeley will ask incoming freshmen this fall to give a DNA sample, which the university says it will use for simple tests to determine alcohol metabolism or lactose intolerance. The program is voluntary and anonymous, but the Center for Genetics and Society, also of Berkeley, cited the Walgreens case as more reason to argue the university ought to stop the program.

Related Content:
DISCOVER: How Much Can You Learn from a Home DNA Test?
80beats: 5 Reasons Walgreens Selling Personal DNA Tests Might Be a Bad Idea
80beats: No Gattaca Here: Genetic Anti-Discrimination Law Goes Into Effect
Discoblog: Welcome, UC Berkeley Freshmen! Now Hand Over Your DNA Samples

Image: Pathway Genomics


Joint Statement From Closed Space Group Meeting

Joint Statement by Space Organizations on the FY 2011 NASA Budget

"We the undersigned, a diverse group of organizations with a vital interest in our Nation's space program, make the following statements:

- We strongly support the top line FY2011 NASA budget.
- We believe an important goal of the NASA budget is to accelerate the development of the intellectual capital of the United States by investing in a high-cadence exciting program.
- We are excited by the increases in science, aeronautics and technology initiatives.
- We believe both human exploration and research are important: destination, milestones, engagement and story matter.
- We believe this is an opportunity for NASA to craft the exploration strategy in partnership with science and applied science that includes the International Space Station, safe and cost-effective access to low earth orbit, robotic precursors, and other missions. Heavy lift launch and in-space servicing enable new realms of exploration and science.
- We believe it is critically important that the American people can and must participate and be engaged in the journey of discovery and exploration."

Presentations From The Closed Space Organization Meeting (Update), earlier post
Meeting of Space Organizations, earlier post

Pardon Me, But Your Star Is Eating My Planet

Posted on HubbleSite today is the story of WASP-12b, a Hot Jupiter discovered April 1, 2008.  WASP-12b has a blistering orbital rate of just over 26 hours.  From HubbleSite:

May 20, 2010: “The Star That Ate My Planet” may sound like a B-grade science fiction movie title, but this is really happening 600 light-years away. Like a moth in a candle flame, a doomed Jupiter-sized planet has moved so close to its sunlike parent star that it is spilling its atmosphere onto the star. This happens because the planet gets so hot that its atmosphere puffs up to the point where the star’s gravity pulls it in. The planet will likely be completely devoured in 10 million years. Observations by Hubble’s new Cosmic Origins Spectrograph measured a variety of elements in the planet’s bloated atmosphere as the planet passed in front of its star. The planet, called WASP-12b, is the hottest known world ever discovered, with an atmosphere seething at 2,800 degrees Fahrenheit.

For the full story, visit HubbleSite. An interesting story about the Milky Way’s hottest known planet.

NASA NOMAD: AT&T Phone Issues

NOMAD Outreach: UPDATE #2: AT&T Mobile Device Issue Under Investigation - Thursday, May 20, 2010

"What Is Happening: The AT&T mobile device issue appears to be more widespread than initially thought. In addition to AT&T iPhones in the Ames Research Center (ARC) and Dryden Flight Research Center (DRFC) areas, users at Goddard Flight Research Center (GSFC), Johnson Space Center (JSC) and in the Denver area are also reporting impacts. The AT&T mobile device issue at JSC is not limited to iPhones. Users from other Centers may also be affected."